diff --git a/.circleci/config.yml b/.circleci/config.yml
index f884388e0a..823c9f3b9d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -73,7 +73,9 @@ jobs:
       - run:
           name: install dependencies
           command: |
-            apt-get update && apt install -y python3-pip
+            apt-get update && apt install -y python3-pip && apt install -y python3-venv
+            python3 -m venv env
+            source env/bin/activate
             python3 -m pip install --upgrade pip
             python3 -m pip install -r  ~/project/requirements.txt
             python3 -m pip install ~/project/tools/schemacode/[render]
@@ -83,6 +85,7 @@ jobs:
       - run:
           name: generate pdf version docs
           command: |
+            source env/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh
             mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf
diff --git a/CODEOWNERS b/CODEOWNERS
index ec56a06da0..54d256bb49 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -5,19 +5,15 @@
 # Request for Review) please add your GitHub username next to the file you want to
 # monitor below.
 
-# Add your GitHub name below to get notified about proposed releases
-/src/CHANGES.md @chrisgorgo @sappelhoff @CPernet
-
 # Individual sections
-/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos
-/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo
-/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan
-/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan
-/src/05-derivatives/03-imaging.md @effigies
-/src/05-derivatives/04-structural-derivatives.md @edickie @ahoopes
-/src/05-derivatives/05-functional-derivatives.md @effigies
-/src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie
-/src/appendices/meg-file-formats.md @monkeyman192
+/src/common-principles.md @chrisgorgo @DimitriPapadopoulos
+/src/modality-specific-files/magnetic-resonance-imaging-data.md @chrisgorgo
+/src/modality-specific-files/electroencephalography.md @sappelhoff @ezemikulan
+/src/modality-specific-files/intracranial-electroencephalography.md @ezemikulan
+/src/derivatives/imaging.md @effigies
+/src/derivatives/structural-derivatives.md @edickie @ahoopes
+/src/derivatives/functional-derivatives.md @effigies
+/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie
 
 # The schema
 /src/schema/ @tsalo @erdalkaraca
diff --git a/mkdocs.yml b/mkdocs.yml
index 0bb0d57ede..cd0564aa27 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,5 +1,48 @@
 site_name: Brain Imaging Data Structure v1.7.1-dev
 site_url: https://bids-specification.readthedocs.io/en/stable/
+nav:
+    - The BIDS Specification:
+      - Introduction: introduction.md
+      - Common principles: common-principles.md
+      - Modality agnostic files: modality-agnostic-files.md
+      - Modality specific files:
+        - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md
+        - Magnetoencephalography: modality-specific-files/magnetoencephalography.md
+        - Electroencephalography: modality-specific-files/electroencephalography.md
+        - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
+        - Task events: modality-specific-files/task-events.md
+        - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md
+        - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
+        - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
+        - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
+        - Microscopy: modality-specific-files/microscopy.md
+        - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
+      - Derivatives:
+        - BIDS Derivatives: derivatives/introduction.md
+        - Common data types and metadata: derivatives/common-data-types.md
+        - Imaging data types: derivatives/imaging.md
+      - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
+      - Glossary: glossary.md
+      - BIDS Extension Proposals: extensions.md
+      - Appendix:
+        - Contributors: appendices/contributors.md
+        - Licenses: appendices/licenses.md
+        - Entity table: appendices/entity-table.md
+        - Entities: appendices/entities.md
+        - File collections: appendices/file-collections.md
+        - Units: appendices/units.md
+        - Hierarchical Event Descriptors: appendices/hed.md
+        - MEG file formats: appendices/meg-file-formats.md
+        - MEG systems: appendices/meg-systems.md
+        - Coordinate systems: appendices/coordinate-systems.md
+        - Quantitative MRI: appendices/qmri.md
+        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
+        - Cross modality correspondence: appendices/cross-modality-correspondence.md
+      - Changelog: CHANGES.md
+    - The BIDS Starter Kit:
+      - Website: https://bids-standard.github.io/bids-starter-kit
+      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
+      - GitHub repository: https://github.com/bids-standard/bids-starter-kit
 theme:
     name: material
     favicon: images/favicon.png
@@ -33,6 +76,25 @@ plugins:
         module_name: tools/mkdocs_macros_bids/main
     - redirects:
         redirect_maps:
+            '01-introduction.md': 'introduction.md'
+            '02-common-principles.md': 'common-principles.md'
+            '03-modality-agnostic-files.md': 'modality-agnostic-files.md'
+            '04-modality-specific-files/01-magnetic-resonance-imaging-data.md': 'modality-specific-files/magnetic-resonance-imaging-data.md'
+            '04-modality-specific-files/02-magnetoencephalography.md': 'modality-specific-files/magnetoencephalography.md'
+            '04-modality-specific-files/03-electroencephalography.md': 'modality-specific-files/electroencephalography.md'
+            '04-modality-specific-files/04-intracranial-electroencephalography.md': 'modality-specific-files/intracranial-electroencephalography.md'
+            '04-modality-specific-files/05-task-events.md': 'modality-specific-files/task-events.md'
+            '04-modality-specific-files/06-physiological-and-other-continuous-recordings.md': 'modality-specific-files/physiological-and-other-continuous-recordings.md'
+            '04-modality-specific-files/07-behavioral-experiments.md': 'modality-specific-files/behavioral-experiments.md'
+            '04-modality-specific-files/08-genetic-descriptor.md': 'modality-specific-files/genetic-descriptor.md'
+            '04-modality-specific-files/09-positron-emission-tomography.md': 'modality-specific-files/positron-emission-tomography.md'
+            '04-modality-specific-files/10-microscopy.md': 'modality-specific-files/microscopy.md'
+            '04-modality-specific-files/11-near-infrared-spectroscopy.md': 'modality-specific-files/near-infrared-spectroscopy.md'
+            '05-derivatives/01-introduction.md': 'derivatives/introduction.md'
+            '05-derivatives/02-common-data-types.md': 'derivatives/common-data-types.md'
+            '05-derivatives/03-imaging.md': 'derivatives/imaging.md'
+            '06-longitudinal-and-multi-site-studies.md': 'longitudinal-and-multi-site-studies.md'
+            '07-extensions.md': 'extensions.md'
             '99-appendices/14-glossary.md': 'glossary.md'
             '99-appendices/01-contributors.md': 'appendices/contributors.md'
             '99-appendices/02-licenses.md': 'appendices/licenses.md'
@@ -49,46 +111,3 @@ plugins:
             '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md'
 docs_dir: 'src'
 use_directory_urls: false
-nav:
-    - The BIDS Specification:
-      - Introduction: 01-introduction.md
-      - Common principles: 02-common-principles.md
-      - Modality agnostic files: 03-modality-agnostic-files.md
-      - Modality specific files:
-        - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md
-        - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md
-        - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md
-        - Intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md
-        - Task events: 04-modality-specific-files/05-task-events.md
-        - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
-        - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md
-        - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
-        - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
-        - Microscopy: 04-modality-specific-files/10-microscopy.md
-        - Near-Infrared Spectroscopy: 04-modality-specific-files/11-near-infrared-spectroscopy.md
-      - Derivatives:
-        - BIDS Derivatives: 05-derivatives/01-introduction.md
-        - Common data types and metadata: 05-derivatives/02-common-data-types.md
-        - Imaging data types: 05-derivatives/03-imaging.md
-      - Longitudinal and multi-site studies: 06-longitudinal-and-multi-site-studies.md
-      - Glossary: glossary.md
-      - BIDS Extension Proposals: 07-extensions.md
-      - Appendix:
-        - Contributors: appendices/contributors.md
-        - Licenses: appendices/licenses.md
-        - Entity table: appendices/entity-table.md
-        - Entities: appendices/entities.md
-        - File collections: appendices/file-collections.md
-        - Units: appendices/units.md
-        - Hierarchical Event Descriptors: appendices/hed.md
-        - MEG file formats: appendices/meg-file-formats.md
-        - MEG systems: appendices/meg-systems.md
-        - Coordinate systems: appendices/coordinate-systems.md
-        - Quantitative MRI: appendices/qmri.md
-        - Arterial Spin Labeling: appendices/arterial-spin-labeling.md
-        - Cross modality correspondence: appendices/cross-modality-correspondence.md
-      - Changelog: CHANGES.md
-    - The BIDS Starter Kit:
-      - Website: https://bids-standard.github.io/bids-starter-kit
-      - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
-      - GitHub repository: https://github.com/bids-standard/bids-starter-kit
diff --git a/pdf_build_src/build_pdf.sh b/pdf_build_src/build_pdf.sh
index 3f1f6a6bd6..51087a4d7f 100755
--- a/pdf_build_src/build_pdf.sh
+++ b/pdf_build_src/build_pdf.sh
@@ -4,20 +4,27 @@
 set -eu
 
 # prepare the copied src directory
+echo "Running: process_markdowns.py"
 python3 process_markdowns.py
 
 # copy pandoc_script into the temp src_copy directory
+echo "Running: copying files to src_copy/src"
 cp pandoc_script.py header.tex cover.tex header_setup.tex src_copy/src
 
 # run pandoc_script from src_copy directory
+echo "Running: cd to src_copy/src and run pandoc_script.py"
 pushd src_copy/src
 python3 pandoc_script.py
+
+echo "Running: Moving built spec PDF and log JSON to pdf_build_src"
 mv bids-spec.pdf ../..
 mv bids-spec_pandoc_log.json ../..
 popd
 
 # Do a check on the pandoc log file
+echo "Running: check_pandoc_log.py"
 python3 check_pandoc_log.py
 
 # delete the duplicated src directory
+echo "Running: remove unneeded src_copy directory"
 rm -rf src_copy
diff --git a/src/CHANGES.md b/src/CHANGES.md
index c888cf78e3..24bc407919 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -489,30 +489,30 @@
 
 -   Added support for MEG data (merged BEP008).
 -   Added `SequenceName` field.
--   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](04-modality-specific-files/05-task-events.md).
--   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](modality-specific-files/task-events.md).
+-   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 -   Added `DwellTime` field.
 
 ## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18)
 
--   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for multiple defacing masks: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for multiple defacing masks: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13)
 
--   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## 1.0.1-rc1
 
--   Added T1 Rho maps: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for phenotypic information split into multiple files: [3.2 Participant key file](03-modality-agnostic-files.md#participants-file).
+-   Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.
diff --git a/src/appendices/arterial-spin-labeling.md b/src/appendices/arterial-spin-labeling.md
index 35b7723806..4d1253eaab 100644
--- a/src/appendices/arterial-spin-labeling.md
+++ b/src/appendices/arterial-spin-labeling.md
@@ -73,7 +73,7 @@ Y. Suzuki and [OSIPI Task force 4.1: ASL lexicon milestone 1](https://osipi.gith
 
 ### (P)CASL sequence
 
-![PCASL](../04-modality-specific-files/images/asl_pcasl_sequence.png)
+![PCASL](../modality-specific-files/images/asl_pcasl_sequence.png)
 
 For (P)CASL, specifying the `LabelingDuration` and the `PostLabelingDelay` is required.
 The `LabelingDuration` is defined as the total duration of the labeling pulse train in seconds.
@@ -89,7 +89,7 @@ whereas in case of `CASL`,the recommended `CASLType` field describes if a separa
 
 ### (P)CASL Labeling Pulses
 
-![PCASL Labeling Pulses](../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png)
+![PCASL Labeling Pulses](../modality-specific-files/images/asl_pcasl_labeling_pulses.png)
 
 Several recommended metadata fields describe the labeling pulses of the labeling pulse train in PCASL.
 The `LabelingPulseAverageGradient` and the `LabelingPulseMaximumGradient` are the average labeling gradient
@@ -101,7 +101,7 @@ and the delay between the peaks of the individual labeling pulses in millisecond
 
 ### PASL sequence
 
-![PASL without Bolus Cut-off](../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png)
+![PASL without Bolus Cut-off](../modality-specific-files/images/asl_pasl_boluscutoff_false.png)
 
 For PASL, specifying the `PostLabelingDelay` is required.
 `PostLabelingDelay` is the time, in seconds, from the middle of the labeling pulse until the middle of
@@ -109,7 +109,7 @@ the excitation pulse applied to the imaging slab (for 3D acquisition) or first s
 Additionally, the `BolusCutOffFlag` field is required,
 which is a boolean indicating if a bolus cut-off technique has been applied.
 
-![PASL QUIPSSII](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
+![PASL QUIPSSII](../modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png)
 
 When `BolusCutOffFlag` is set true for `PASL`, two additional metadata fields are required:
 `BolusCutOffTechnique` and `BolusCutOffDelay`.
@@ -117,7 +117,7 @@ In this example, the `BolusCutOffTechnique`, which is the name of the technique
 is QUIPSS-II consisting of only one bolus cut-off pulse.
 The `BolusCutOffDelay` is therefore a number, representing the duration between the end of the labeling and the start of the bolus cut-off saturation pulse, in seconds.
 
-![PASL Q2TIPS](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
+![PASL Q2TIPS](../modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png)
 
 In this example, the `BolusCutOffTechnique` applied is Q2TIPS, consisting of multiple bolus cut-off pulses.
 In this case, only the duration of the first and last pulse should be specified in `BolusCutOffDelay`.
@@ -127,4 +127,4 @@ In this case, only the duration of the first and last pulse should be specified
 The specification includes a dependency table, describing metadata field dependencies for ASL.
 This flowchart is intended to further clarify that table.
 
-![ASL Flowchart](../04-modality-specific-files/images/asl_flowchart.png)
+![ASL Flowchart](../modality-specific-files/images/asl_flowchart.png)
diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
index 91273835c7..e48615eae7 100644
--- a/src/appendices/coordinate-systems.md
+++ b/src/appendices/coordinate-systems.md
@@ -249,6 +249,6 @@ Please note that `space-scanner` SHOULD NOT be used, it is mentioned in this spe
 
 <!-- Link Definitions -->
 
-[common file level metadata fields]: ../05-derivatives/02-common-data-types.md#common-file-level-metadata-fields
+[common file level metadata fields]: ../derivatives/common-data-types.md#common-file-level-metadata-fields
 
-[deprecated]: ../02-common-principles.md#definitions
+[deprecated]: ../common-principles.md#definitions
diff --git a/src/appendices/cross-modality-correspondence.md b/src/appendices/cross-modality-correspondence.md
index f77598d147..c71a1c73f5 100644
--- a/src/appendices/cross-modality-correspondence.md
+++ b/src/appendices/cross-modality-correspondence.md
@@ -7,7 +7,7 @@ please pay specific attention to the format the MR images are in.
 It is important to note whether the MR images have been unwarped
 in order to correct for gradient non-linearities,
 indicated by the `NonlinearGradientCorrection` metadata field
-(see [Magnetic Resonance Imaging Data - Sequence Specifics](../04-modality-specific-files/01-magnetic-resonance-imaging-data.md#sequence-specifics)).
+(see [Magnetic Resonance Imaging Data - Sequence Specifics](../modality-specific-files/magnetic-resonance-imaging-data.md#sequence-specifics)).
 The reason for this is that the MRI needs to be corrected for nonlinear gradients
 in order to fit the accompanying PET scans for co-registration
 (Knudsen et al. 2020, [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433);
diff --git a/src/appendices/entities.md b/src/appendices/entities.md
index 06101ce0d0..3e9605a9d8 100644
--- a/src/appendices/entities.md
+++ b/src/appendices/entities.md
@@ -4,7 +4,7 @@ This section compiles the entities (key-value pairs within file names) described
 specification, and describes each.
 
 A general introduction to entities is given in the section on
-[filename structure](../02-common-principles.md#file-name-structure).
+[filename structure](../common-principles.md#file-name-structure).
 
 The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT
 be specified for a given file type, is specified in the [Entity Table](entity-table.md).
diff --git a/src/appendices/entity-table.md b/src/appendices/entity-table.md
index f07c69982b..1a4ff0fffd 100644
--- a/src/appendices/entity-table.md
+++ b/src/appendices/entity-table.md
@@ -10,7 +10,7 @@ Entity formats indicate whether the value is alphanumeric
 (`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on
-[filename structure](../02-common-principles.md#file-name-structure),
+[filename structure](../common-principles.md#file-name-structure),
 while entity definitions are in the [Entities Appendix](entities.md).
 
 <!--
diff --git a/src/appendices/file-collections.md b/src/appendices/file-collections.md
index 56c675f2ec..4228e5cebe 100644
--- a/src/appendices/file-collections.md
+++ b/src/appendices/file-collections.md
@@ -1,6 +1,6 @@
 # File collections
 
-Here, some concrete use-cases of [entity-linked file collections](../02-common-principles.md#file-name-structure) are listed using descriptive tables, organized by modality.
+Here, some concrete use-cases of [entity-linked file collections](../common-principles.md#file-name-structure) are listed using descriptive tables, organized by modality.
 
 The tables in this appendix catalog applications where the use of
 a file collection is REQUIRED.
diff --git a/src/appendices/hed.md b/src/appendices/hed.md
index 77677a00ab..37bb9a3594 100644
--- a/src/appendices/hed.md
+++ b/src/appendices/hed.md
@@ -35,7 +35,7 @@ on GitHub.
 
 Event-related data in BIDS appears in tab-separated value (`events.tsv`)
 files in various places in the dataset hierarchy
-(see [Events](../04-modality-specific-files/05-task-events.md)).
+(see [Events](../modality-specific-files/task-events.md)).
 
 `events.tsv` files MUST have `onset` and `duration` columns.
 Dataset curators MAY also include additional columns and define their
@@ -152,7 +152,7 @@ If possible, users should annotate these columns in a single
 If some recordings in the dataset have a column whose values deviate from a
 standard pattern, then the annotations for that column MUST be placed in
 sidecars located deeper in the dataset directory hierarchy.
-According to the BIDS [Inheritance Principle](../02-common-principles.md#the-inheritance-principle),
+According to the BIDS [Inheritance Principle](../common-principles.md#the-inheritance-principle),
 once a column key in a sidecar (that is, the column name found in the `events.tsv` files) is set,
 information about that column cannot be overridden by a sidecar appearing in a directory
 closer to the dataset root.
diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md
index 8da4d31edb..2cf0daadcb 100644
--- a/src/appendices/meg-file-formats.md
+++ b/src/appendices/meg-file-formats.md
@@ -212,7 +212,7 @@ entity to indicate each part.
 If there are multiple parts of a recording and the optional `scans.tsv` is provided,
 remember to list all files separately in `scans.tsv` and that the entries
 for the `acq_time` column in `scans.tsv` MUST all be identical, as described in
-[Scans file](../03-modality-agnostic-files.md#scans-file).
+[Scans file](../modality-agnostic-files.md#scans-file).
 
 Example:
 
diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md
index dba3c65243..ceaa57d645 100644
--- a/src/appendices/qmri.md
+++ b/src/appendices/qmri.md
@@ -35,7 +35,7 @@ There are two main ways to obtain a quantitative map:
 
 ### Inputs are file collections
 
-The common concept of [entity-linked file collections](../02-common-principles.md#entity-linked-file-collections) enables the description of a qMRI
+The common concept of [entity-linked file collections](../common-principles.md#entity-linked-file-collections) enables the description of a qMRI
 application by creating logical groups of input files through `suffix` and certain entities
 representing acquisition parameters (`echo`, `flip`, `inv`, `mt`) or file parts (`part`).
 
@@ -208,7 +208,7 @@ Explanation of the table:
 ### Metadata requirements for qMRI maps
 
 As qMRI maps are stored as derivatives, they are subjected to the metadata requirements of
-[derived datasets](../03-modality-agnostic-files.md#derived-dataset-and-pipeline-description).
+[derived datasets](../modality-agnostic-files.md#derived-dataset-and-pipeline-description).
 
 An example `dataset_description.json` for a qMRI map derivatives directory:
 
diff --git a/src/appendices/units.md b/src/appendices/units.md
index a375892366..baceceaf2b 100644
--- a/src/appendices/units.md
+++ b/src/appendices/units.md
@@ -1,6 +1,6 @@
 # Units
 
-As described in the [Units](../02-common-principles.md#units),
+As described in the [Units](../common-principles.md#units),
 the specification of units SHOULD follow the
 [International System of Units](https://en.wikipedia.org/wiki/International_System_of_Units)
 (SI, abbreviated from the French Système international (d'unités)).
@@ -10,7 +10,7 @@ for encoding units is RECOMMENDED to achieve maximum portability and limited
 variability of representation.
 If a CMIXF-12 representation of a unit is not possible, the unit can be declared
 as custom units and defined in an accompanying JSON file, as described in the
-[units section](../02-common-principles.md#units).
+[units section](../common-principles.md#units).
 Earlier versions of the BIDS standard listed the following Unicode symbols, and
 these are still included for backwards compatibility:
 
@@ -27,7 +27,7 @@ It is RECOMMENDED that units be CMIXF-12 compliant or among these five Unicode
 characters.
 Please note the appropriate upper- or lower- casing when using CMIXF-12.
 
-For cases that are unspecified by this appendix or the [units section](../02-common-principles.md#units),
+For cases that are unspecified by this appendix or the [units section](../common-principles.md#units),
 the [CMIXF-12](https://people.csail.mit.edu/jaffer/MIXF/CMIXF-12) convention
 applies.
 
diff --git a/src/02-common-principles.md b/src/common-principles.md
similarity index 98%
rename from src/02-common-principles.md
rename to src/common-principles.md
index 8fb609a526..137c595cf7 100644
--- a/src/02-common-principles.md
+++ b/src/common-principles.md
@@ -90,7 +90,7 @@ Data for each subject are placed in subdirectories named "`sub-<label>`",
 where string "`<label>`" is substituted with the unique identification
 label of each subject.
 Additional information on each participant MAY be provided in a
-[participants file](03-modality-agnostic-files.md#participants-file)
+[participants file](modality-agnostic-files.md#participants-file)
 in the root directory of the dataset.
 
 If data for the subject were acquired across multiple sessions, then within
@@ -100,7 +100,7 @@ label for each session.
 In datasets where at least one subject has more than one session, this
 additional subdirectory later SHOULD be added for all subjects in the dataset.
 Additional information on each session MAY be provided in a
-[sessions file](03-modality-agnostic-files.md#sessions-file)
+[sessions file](modality-agnostic-files.md#sessions-file)
 within the subject directory.
 
 Within the session subdirectory (or the subject subdirectory if no
@@ -387,7 +387,7 @@ Tabular data MUST be saved as tab delimited values (`.tsv`) files, that is, CSV
 files where commas are replaced by tabs. Tabs MUST be true tab characters and
 MUST NOT be a series of space characters. Each TSV file MUST start with a header
 line listing the names of all columns (with the exception of
-[physiological and other continuous recordings](04-modality-specific-files/06-physiological-and-other-continuous-recordings.md)).
+[physiological and other continuous recordings](modality-specific-files/physiological-and-other-continuous-recordings.md)).
 It is RECOMMENDED that the column names in the header of the TSV file are
 written in [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) with the
 first letter in lower case (for example, `variable_name`, not `Variable_name`).
@@ -499,7 +499,7 @@ Example of a hypothetical `*_bold.json` file, accompanying a `*_bold.nii` file:
 Example of a hypothetical `*_events.json` file, accompanying an
 `*_events.tsv` file. Note that the JSON file contains a key describing an
 *arbitrary* column `stim_presentation_side` in the TSV file it accompanies.
-See [task events section](04-modality-specific-files/05-task-events.md)
+See [task events section](modality-specific-files/task-events.md)
 for more information.
 
 ```JSON
@@ -532,7 +532,8 @@ for more information.
 1.  If multiple metadata files satisfy criteria 2.a-c above:
 
     1.  For [tabular files](#tabular-files) and other simple metadata files
-        (for instance, [`bvec` / `bval` files for diffusion MRI](#04-modality-specific-files/01-magnetic-resonance-imaging#required-gradient-orientation-information)),
+        (for instance,
+        [`bvec` / `bval` files for diffusion MRI](modality-specific-files/magnetic-resonance-imaging-data.md#required-gradient-orientation-information)),
         accessing metadata associated with a data file MUST consider only the
         applicable file that is lowest in the filesystem hierarchy.
 
@@ -680,7 +681,7 @@ A guide for using macros can be found at
 BIDS allows for custom user-defined `<label>`s and `<index>`es for example,
 for naming of participants, sessions, acquisition schemes.
 Note that they MUST consist only of allowed characters as described in
-[Definitions](02-common-principles.md#definitions) above.
+[Definitions](common-principles.md#definitions) above.
 In `<index>`es we RECOMMEND using zero padding (for example, `01` instead of `1`
 if you have more than nine subjects) to make alphabetical sorting more intuitive.
 Note that zero padding SHOULD NOT be used to merely maintain uniqueness
@@ -955,8 +956,8 @@ to suppress warnings or provide interpretations of your filenames.
 
 <!-- Link Definitions -->
 
-[dataset-description]: 03-modality-agnostic-files.md#dataset-description
-[dataset_description.json]: 03-modality-agnostic-files.md#dataset_descriptionjson
-[derived-dataset-description]: 03-modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[dataset-description]: modality-agnostic-files.md#dataset-description
+[dataset_description.json]: modality-agnostic-files.md#dataset_descriptionjson
+[derived-dataset-description]: modality-agnostic-files.md#derived-dataset-and-pipeline-description
 [deprecated]: #definitions
 [uris]: #uniform-resource-indicator
diff --git a/src/05-derivatives/02-common-data-types.md b/src/derivatives/common-data-types.md
similarity index 96%
rename from src/05-derivatives/02-common-data-types.md
rename to src/derivatives/common-data-types.md
index ac672f64e0..ea3c6a2e6e 100644
--- a/src/05-derivatives/02-common-data-types.md
+++ b/src/derivatives/common-data-types.md
@@ -4,7 +4,7 @@
 
 Each derivative data file SHOULD be described by a JSON file provided as a sidecar
 or higher up in the hierarchy of the derived dataset (according to the
-[Inheritance Principle](../02-common-principles.md#the-inheritance-principle))
+[Inheritance Principle](../common-principles.md#the-inheritance-principle))
 unless a particular derivative includes REQUIRED metadata fields, in which case a
 JSON file is also REQUIRED.
 Each derivative type defines their own set of fields, but all of them
@@ -262,10 +262,10 @@ static volume, a `RepetitionTime` property would no longer be relevant).
 
 [object]: https://www.json.org/json-en.html
 
-[bids uris]: ../02-common-principles.md#bids-uri
+[bids uris]: ../common-principles.md#bids-uri
 
-[deprecated]: ../02-common-principles.md#definitions
+[deprecated]: ../common-principles.md#definitions
 
-[uris]: ../02-common-principles.md#uniform-resource-indicator
+[uris]: ../common-principles.md#uniform-resource-indicator
 
-[uri]: ../02-common-principles.md#uniform-resource-indicator
+[uri]: ../common-principles.md#uniform-resource-indicator
diff --git a/src/05-derivatives/03-imaging.md b/src/derivatives/imaging.md
similarity index 99%
rename from src/05-derivatives/03-imaging.md
rename to src/derivatives/imaging.md
index a320448308..b80ab2c70b 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/derivatives/imaging.md
@@ -547,6 +547,6 @@ index   name                abbreviation
 
 <!-- Link Definitions -->
 
-[common_preproc]: 02-common-data-types.md#preprocessed-or-cleaned-data
+[common_preproc]: common-data-types.md#preprocessed-or-cleaned-data
 
-[unspecified]: ../02-common-principles.md#unspecified-data
+[unspecified]: ../common-principles.md#unspecified-data
diff --git a/src/05-derivatives/01-introduction.md b/src/derivatives/introduction.md
similarity index 92%
rename from src/05-derivatives/01-introduction.md
rename to src/derivatives/introduction.md
index 195422f9e0..9f1d66d436 100644
--- a/src/05-derivatives/01-introduction.md
+++ b/src/derivatives/introduction.md
@@ -19,7 +19,7 @@ in [Derived dataset and pipeline description][derived-dataset-description].
     types of files, there may be one or more required metadata fields, in which
     case at least one metadata file containing that field must be located
     somewhere within the file’s hierarchy (per the
-    [Inheritance Principle](../02-common-principles.md#the-inheritance-principle)).
+    [Inheritance Principle](../common-principles.md#the-inheritance-principle)).
 
 -   When chaining derivative pipelines, any JSON fields that were specified as
     mandatory in the input files SHOULD be propagated forward in the output
@@ -72,8 +72,8 @@ in [Derived dataset and pipeline description][derived-dataset-description].
 
 <!-- Link Definitions -->
 
-[definitions]: ../02-common-principles.md#definitions
+[definitions]: ../common-principles.md#definitions
 
-[storage]: ../02-common-principles.md#storage-of-derived-datasets
+[storage]: ../common-principles.md#storage-of-derived-datasets
 
-[derived-dataset-description]: ../03-modality-agnostic-files.md#derived-dataset-and-pipeline-description
+[derived-dataset-description]: ../modality-agnostic-files.md#derived-dataset-and-pipeline-description
diff --git a/src/07-extensions.md b/src/extensions.md
similarity index 100%
rename from src/07-extensions.md
rename to src/extensions.md
diff --git a/src/index.md b/src/index.md
index 91f3aa6e44..ade6162157 100644
--- a/src/index.md
+++ b/src/index.md
@@ -11,7 +11,7 @@ data.
 If BIDS is new to you, and you would like to learn more about how to adapt your
 own datasets to match the BIDS specification, we recommend exploring the
 [BIDS Starter Kit](https://bids-standard.github.io/bids-starter-kit/).
-Alternatively, to get started please read [the introduction to the specification](01-introduction.md).
+Alternatively, to get started please read [the introduction to the specification](introduction.md).
 
 For an overview of the BIDS ecosystem, visit the [BIDS homepage](https://bids.neuroimaging.io).
 The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.3686061).
diff --git a/src/01-introduction.md b/src/introduction.md
similarity index 99%
rename from src/01-introduction.md
rename to src/introduction.md
index 9cfd3fe5ef..ba53879f0e 100644
--- a/src/01-introduction.md
+++ b/src/introduction.md
@@ -49,7 +49,7 @@ different backgrounds.
 The BIDS specification can be extended in a backwards compatible way and will
 evolve over time. This is accomplished through community-driven BIDS Extension
 Proposals (BEPs). For more information about the BEP process, see
-[Extending the BIDS specification](07-extensions.md).
+[Extending the BIDS specification](extensions.md).
 
 ## Citing BIDS
 
diff --git a/src/06-longitudinal-and-multi-site-studies.md b/src/longitudinal-and-multi-site-studies.md
similarity index 96%
rename from src/06-longitudinal-and-multi-site-studies.md
rename to src/longitudinal-and-multi-site-studies.md
index e7abffbe40..5f114b2534 100644
--- a/src/06-longitudinal-and-multi-site-studies.md
+++ b/src/longitudinal-and-multi-site-studies.md
@@ -1,9 +1,9 @@
 # Longitudinal and multi-site studies
 
 Multiple sessions (visits) are encoded by adding an extra layer of directories
-and [filenames](02-common-principles.md#file-name-structure)
+and [filenames](common-principles.md#file-name-structure)
 in the form of a session (for example `ses-<label>`) and
-with a [`*_sessions.tsv` file](03-modality-agnostic-files.md#sessions-file).
+with a [`*_sessions.tsv` file](modality-agnostic-files.md#sessions-file).
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
diff --git a/src/03-modality-agnostic-files.md b/src/modality-agnostic-files.md
similarity index 96%
rename from src/03-modality-agnostic-files.md
rename to src/modality-agnostic-files.md
index 4921118b9e..4efeae0188 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/modality-agnostic-files.md
@@ -244,7 +244,7 @@ sub-03 33 F n/a read
 
 It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
 `participants.json` file to describe the TSV column names and properties of their values (see also
-the [section on tabular files](02-common-principles.md#tabular-files)).
+the [section on tabular files](common-principles.md#tabular-files)).
 Such sidecar files are needed to interpret the data, especially so when
 optional columns are defined beyond `age`, `sex`, `handedness`, `species`, `strain`,
 and `strain_rrid`, such as `group` in this example, or when a different
@@ -318,7 +318,7 @@ sample-05 sub-02 tissue n/a
 
 It is RECOMMENDED to accompany each `samples.tsv` file with a sidecar
 `samples.json` file to describe the TSV column names and properties of their values
-(see also the [section on tabular files](02-common-principles.md#tabular-files)).
+(see also the [section on tabular files](common-principles.md#tabular-files)).
 
 `samples.json` example:
 
@@ -361,7 +361,7 @@ in the BIDS dataset and `participants.tsv` file.
 
 As with all other tabular data, the additional phenotypic information files
 MAY be accompanied by a JSON file describing the columns in detail
-(see [Tabular files](02-common-principles.md#tabular-files)).
+(see [Tabular files](common-principles.md#tabular-files)).
 
 In addition to the column descriptions, the JSON file MAY contain the following fields:
 
@@ -446,7 +446,7 @@ and not the individual files in that directory.
 Some neural recordings consist of multiple parts,
 that span several files,
 but that share the same extension.
-For example in [entity-linked file collections](./02-common-principles.md#entity-linked-file-collections),
+For example in [entity-linked file collections](./common-principles.md#entity-linked-file-collections),
 commonly used for qMRI,
 where recordings may be linked through entities such as `echo` and `part`
 (using `.nii` or `.nii.gz` extensions).
@@ -469,7 +469,7 @@ For example vigilance questionnaire score administered after a resting
 state scan.
 All such included additional fields SHOULD be documented in an accompanying
 `_scans.json` file that describes these fields in detail
-(see [Tabular files](02-common-principles.md#tabular-files)).
+(see [Tabular files](common-principles.md#tabular-files)).
 
 Example `_scans.tsv`:
 
@@ -497,7 +497,7 @@ In case of multiple sessions there is an option of adding additional
 In such case one file per participant SHOULD be added.
 These files MUST include a `session_id` column and describe each session by one and only one row.
 Column names in `sessions.tsv` files MUST be different from group level participant key column names in the
-[`participants.tsv` file](./03-modality-agnostic-files.md#participants-file).
+[`participants.tsv` file](./modality-agnostic-files.md#participants-file).
 
 <!-- This block generates a columns table.
 The definitions of these fields can be found in
@@ -523,7 +523,7 @@ Template: `code/*`
 Source code of scripts that were used to prepare the dataset MAY be stored here.
 Examples include anonymization or defacing of the data, or
 the conversion from the format of the source data to the BIDS format
-(see [source vs. raw vs. derived data](./02-common-principles.md#source-vs-raw-vs-derived-data)).
+(see [source vs. raw vs. derived data](./common-principles.md#source-vs-raw-vs-derived-data)).
 Extra care should be taken to avoid including original IDs or
 any identifiable information with the source code.
 There are no limitations or recommendations on the language and/or
@@ -531,10 +531,10 @@ code organization of these scripts at the moment.
 
 <!-- Link Definitions -->
 
-[bids uris]: ./02-common-principles.md#bids-uri
+[bids uris]: ./common-principles.md#bids-uri
 
 [object]: https://www.json.org/json-en.html
 
 [string]: https://www.w3schools.com/js/js_json_datatypes.asp
 
-[uri]: ./02-common-principles.md#uniform-resource-indicator
+[uri]: ./common-principles.md#uniform-resource-indicator
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/modality-specific-files/behavioral-experiments.md
similarity index 96%
rename from src/04-modality-specific-files/07-behavioral-experiments.md
rename to src/modality-specific-files/behavioral-experiments.md
index 50e025a0a8..0a31ea5d74 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/modality-specific-files/behavioral-experiments.md
@@ -36,7 +36,7 @@ stimulation turned on or off, the data files may be labelled
 
 In addition to the metadata that is either:
 
--   RECOMMENDED for sidecar JSON files for [tabular data](../02-common-principles.md#tabular-data), or
+-   RECOMMENDED for sidecar JSON files for [tabular data](../common-principles.md#tabular-data), or
 
 -   REQUIRED for some data that can be found in the `beh` directory
     (for example `SamplingFrequency` and `StartTime` for `*_<physio|stim>.tsv.gz` files),
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/modality-specific-files/electroencephalography.md
similarity index 97%
rename from src/04-modality-specific-files/03-electroencephalography.md
rename to src/modality-specific-files/electroencephalography.md
index 662872f594..50c38868da 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/modality-specific-files/electroencephalography.md
@@ -1,8 +1,8 @@
 # Electroencephalography
 
 Support for Electroencephalography (EEG) was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -41,7 +41,7 @@ format. It is furthermore discouraged to use the other accepted formats over
 these RECOMMENDED formats, particularly because there are conversion scripts
 available in most commonly used programming languages to convert data into the
 RECOMMENDED formats. The data in their original format, if different from the
-supported formats, can be stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+supported formats, can be stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).
 
 The original data format is especially valuable in case conversion elicits the
 loss of crucial metadata specific to manufacturers and specific EEG systems. We
@@ -176,8 +176,8 @@ A guide for using macros can be found at
 ```
 
 Note that the date and time information SHOULD be stored in the Study key file
-([`scans.tsv`](../03-modality-agnostic-files.md#scans-file)).
-Date time information MUST be expressed as indicated in [Units](../02-common-principles.md#units)
+([`scans.tsv`](../modality-agnostic-files.md#scans-file)).
+Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 ## Channels description (`*_channels.tsv`)
 
@@ -196,13 +196,13 @@ To avoid confusion, the channels SHOULD be listed in the order they appear in th
 Any number of additional columns MAY be added to provide additional information about the channels.
 
 Note that electrode positions SHOULD NOT be added to this file, but to
-[`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).
+[`*_electrodes.tsv`](./electroencephalography.md#electrodes-description-_electrodestsv).
 Furthermore, the entries in `*_electrodes.tsv` and `*_channels.tsv` do not have to match exactly,
 as for example in the case of recording a single `EOG` channel from a bipolar referencing scheme
 of two electrodes, or a data channel originating from an auxiliary, non-electrode device.
 That is, in most cases `*_electrodes.tsv` will have more entries than `*_channels.tsv`.
 See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in
-["Electrodes description"](./03-electroencephalography.md#electrodes-description-_electrodestsv).
+["Electrodes description"](./electroencephalography.md#electrodes-description-_electrodestsv).
 
 The columns of the channels description table stored in `*_channels.tsv` are:
 
@@ -321,7 +321,7 @@ anatomical landmarks, and the coordinate system and units in which the position
 of electrodes and landmarks is expressed. **The `*_coordsystem.json` is
 REQUIRED if the optional `*_electrodes.tsv` is specified**. If a corresponding
 anatomical MRI is available, the locations of landmarks and fiducials according
-to that scan should also be stored in the [`*_T1w.json`](./01-magnetic-resonance-imaging-data.md)
+to that scan should also be stored in the [`*_T1w.json`](./magnetic-resonance-imaging-data.md)
 file which goes alongside the MRI data.
 
 For disambiguation, we employ the following definitions for fiducials and
diff --git a/src/04-modality-specific-files/08-genetic-descriptor.md b/src/modality-specific-files/genetic-descriptor.md
similarity index 94%
rename from src/04-modality-specific-files/08-genetic-descriptor.md
rename to src/modality-specific-files/genetic-descriptor.md
index 58f9301dcc..e52fc986c3 100644
--- a/src/04-modality-specific-files/08-genetic-descriptor.md
+++ b/src/modality-specific-files/genetic-descriptor.md
@@ -1,8 +1,8 @@
 # Genetic Descriptor
 
 Support genetic descriptors was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -20,7 +20,7 @@ and can be used for practical guidance when curating a new dataset.
 ## Dataset Description
 
 Genetic descriptors are encoded as an additional, OPTIONAL entry in the
-[`dataset_description.json`](../03-modality-agnostic-files.md#dataset_descriptionjson)
+[`dataset_description.json`](../modality-agnostic-files.md#dataset_descriptionjson)
 file.
 
 Datasets linked to a genetic database entry include the following REQUIRED or OPTIONAL
@@ -71,7 +71,7 @@ in the `participants.tsv` file by adding optional columns (like `idh_mutation` i
 example below).
 Note that optional columns MUST be further described in an accompanying
 `participants.json` file as described in
-[Tabular files](../02-common-principles.md#tabular-files).
+[Tabular files](../common-principles.md#tabular-files).
 
 `participants.tsv` example:
 
diff --git a/src/04-modality-specific-files/images/PET_scan_overview.png b/src/modality-specific-files/images/PET_scan_overview.png
similarity index 100%
rename from src/04-modality-specific-files/images/PET_scan_overview.png
rename to src/modality-specific-files/images/PET_scan_overview.png
diff --git a/src/04-modality-specific-files/images/PET_scan_overview.svg b/src/modality-specific-files/images/PET_scan_overview.svg
similarity index 100%
rename from src/04-modality-specific-files/images/PET_scan_overview.svg
rename to src/modality-specific-files/images/PET_scan_overview.svg
diff --git a/src/04-modality-specific-files/images/asl_flowchart.png b/src/modality-specific-files/images/asl_flowchart.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_flowchart.png
rename to src/modality-specific-files/images/asl_flowchart.png
diff --git a/src/04-modality-specific-files/images/asl_pasl_boluscutoff_false.png b/src/modality-specific-files/images/asl_pasl_boluscutoff_false.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_pasl_boluscutoff_false.png
rename to src/modality-specific-files/images/asl_pasl_boluscutoff_false.png
diff --git a/src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png b/src/modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png
rename to src/modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png
diff --git a/src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png b/src/modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png
rename to src/modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png
diff --git a/src/04-modality-specific-files/images/asl_pcasl_labeling_pulses.png b/src/modality-specific-files/images/asl_pcasl_labeling_pulses.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_pcasl_labeling_pulses.png
rename to src/modality-specific-files/images/asl_pcasl_labeling_pulses.png
diff --git a/src/04-modality-specific-files/images/asl_pcasl_sequence.png b/src/modality-specific-files/images/asl_pcasl_sequence.png
similarity index 100%
rename from src/04-modality-specific-files/images/asl_pcasl_sequence.png
rename to src/modality-specific-files/images/asl_pcasl_sequence.png
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes1.png b/src/modality-specific-files/images/ieeg_electrodes1.png
similarity index 100%
rename from src/04-modality-specific-files/images/ieeg_electrodes1.png
rename to src/modality-specific-files/images/ieeg_electrodes1.png
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes2.png b/src/modality-specific-files/images/ieeg_electrodes2.png
similarity index 100%
rename from src/04-modality-specific-files/images/ieeg_electrodes2.png
rename to src/modality-specific-files/images/ieeg_electrodes2.png
diff --git a/src/04-modality-specific-files/images/microscopy_chunks1.png b/src/modality-specific-files/images/microscopy_chunks1.png
similarity index 100%
rename from src/04-modality-specific-files/images/microscopy_chunks1.png
rename to src/modality-specific-files/images/microscopy_chunks1.png
diff --git a/src/04-modality-specific-files/images/microscopy_chunks2.png b/src/modality-specific-files/images/microscopy_chunks2.png
similarity index 100%
rename from src/04-modality-specific-files/images/microscopy_chunks2.png
rename to src/modality-specific-files/images/microscopy_chunks2.png
diff --git a/src/04-modality-specific-files/images/microscopy_sem_overview.jpg b/src/modality-specific-files/images/microscopy_sem_overview.jpg
similarity index 100%
rename from src/04-modality-specific-files/images/microscopy_sem_overview.jpg
rename to src/modality-specific-files/images/microscopy_sem_overview.jpg
diff --git a/src/04-modality-specific-files/images/sub-0001_ses-001_acq-NAS_photo.jpg b/src/modality-specific-files/images/sub-0001_ses-001_acq-NAS_photo.jpg
similarity index 100%
rename from src/04-modality-specific-files/images/sub-0001_ses-001_acq-NAS_photo.jpg
rename to src/modality-specific-files/images/sub-0001_ses-001_acq-NAS_photo.jpg
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
similarity index 98%
rename from src/04-modality-specific-files/04-intracranial-electroencephalography.md
rename to src/modality-specific-files/intracranial-electroencephalography.md
index abb990e3f0..4928376bdc 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -1,8 +1,8 @@
 # Intracranial Electroencephalography
 
 Support for Intracranial Electroencephalography (iEEG) was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -56,7 +56,7 @@ in case conversion elicits the loss of crucial metadata specific to
 manufacturers and specific iEEG systems. We also encourage users to provide
 additional meta information extracted from the manufacturer-specific data files
 in the sidecar JSON file. Other relevant files MAY be included alongside the
-original iEEG data in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+original iEEG data in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).
 
 Note the RecordingType, which depends on whether the data stream on disk is interrupted or not.
 Continuous data is by definition 1 segment without interruption.
@@ -163,8 +163,8 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table("ieeg.iEEGOptional") }}
 
 Note that the date and time information SHOULD be stored in the study key file
-([`scans.tsv`](../03-modality-agnostic-files.md#scans-file)).
-Date time information MUST be expressed as indicated in [Units](../02-common-principles.md#units)
+([`scans.tsv`](../modality-agnostic-files.md#scans-file)).
+Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 #### Example `*_ieeg.json`
 
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
similarity index 98%
rename from src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
rename to src/modality-specific-files/magnetic-resonance-imaging-data.md
index 823ec56f5f..019f4b5258 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -161,7 +161,7 @@ A guide for using macros can be found at
 When adding additional metadata please use the CamelCase version of
 [DICOM ontology terms](https://scicrunch.org/scicrunch/interlex/dashboard)
 whenever possible. See also
-[recommendations on JSON files](../02-common-principles.md#keyvalue-files-dictionaries).
+[recommendations on JSON files](../common-principles.md#keyvalue-files-dictionaries).
 
 ## Anatomy imaging data
 
@@ -301,7 +301,7 @@ and a guide for using macros can be found at
 }}
 
 Parametric images listed in the table above are typically generated by
-processing a [file collection](../02-common-principles.md#entity-linked-file-collections).
+processing a [file collection](../common-principles.md#entity-linked-file-collections).
 Please visit the [file collections appendix](../appendices/file-collections.md) to see the
 list of suffixes available for quantitative MRI (qMRI) applications associated
 with these maps.
@@ -401,7 +401,7 @@ field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
 For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles.md#definitions).
+(`_phase`) data, but the `_phase` suffix is [deprecated](../common-principles.md#definitions).
 Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed
 from the specification in the next major release.
 For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.
@@ -598,9 +598,9 @@ The REQUIRED gradient orientation information corresponding to a DWI acquisition
 MUST be stored using `[*_]dwi.bval` and `[*_]dwi.bvec` pairs of files.
 The `[*_]dwi.bval` and `[*_]dwi.bvec` files MAY be saved on any level of the directory structure
 and thus define those values for all sessions and/or subjects in one place (see
-[the inheritance principle](../02-common-principles.md#the-inheritance-principle)).
+[the inheritance principle](../common-principles.md#the-inheritance-principle)).
 
-As an exception to the [common principles](../02-common-principles.md#definitions)
+As an exception to the [common principles](../common-principles.md#definitions)
 that parameters are constant across runs, the gradient table information (stored
 within the `[*_]dwi.bval` and `[*_]dwi.bvec` files) MAY change across DWI runs.
 
@@ -1151,7 +1151,7 @@ The [`dir-<label>`](../appendices/entities.md#dir) entity is REQUIRED
 for these files.
 This entity MUST be used in addition to
 the REQUIRED `PhaseEncodingDirection` metadata field
-(see [File name structure](../02-common-principles.md#file-name-structure)).
+(see [File name structure](../common-principles.md#file-name-structure)).
 
 Required fields:
 
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
similarity index 98%
rename from src/04-modality-specific-files/02-magnetoencephalography.md
rename to src/modality-specific-files/magnetoencephalography.md
index 3c66ec92ce..9b7180589c 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/modality-specific-files/magnetoencephalography.md
@@ -1,8 +1,8 @@
 # Magnetoencephalography
 
 Support for Magnetoencephalography (MEG) was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -64,7 +64,7 @@ with split files.
 If there are multiple parts of a recording and the optional `scans.tsv` is provided,
 remember to list all files separately in `scans.tsv` and that the entries for the
 `acq_time` column in `scans.tsv` MUST all be identical, as described in
-[Scans file](../03-modality-agnostic-files.md#scans-file).
+[Scans file](../modality-agnostic-files.md#scans-file).
 
 Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh system,
 which saves the MEG sensor coil positions in a separate file with two possible filename extensions  (`.sqd`, `.mrk`).
@@ -87,7 +87,7 @@ that have to be performed to before the MEG data can actually be exploited.
 
 Note that if EEG is recorded with a separate amplifier,
 it SHOULD be stored separately under a new `/eeg` data type
-(see [the EEG specification](03-electroencephalography.md)).
+(see [the EEG specification](electroencephalography.md)).
 
 If however EEG is recorded simultaneously **with the same MEG system**,
 it MAY be stored under the `/meg` data type.
@@ -196,8 +196,8 @@ A guide for using macros can be found at
 ```
 
 Note that the date and time information SHOULD be stored in the Study key file
-(`scans.tsv`), see [Scans file](../03-modality-agnostic-files.md#scans-file).
-Date time information MUST be expressed as indicated in [Units](../02-common-principles.md#units)
+(`scans.tsv`), see [Scans file](../modality-agnostic-files.md#scans-file).
+Date time information MUST be expressed as indicated in [Units](../common-principles.md#units)
 
 ## Channels description (`*_channels.tsv`)
 
@@ -367,7 +367,7 @@ It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical
 landmarks for co-registration of MEG with structural MRI are stored in the
 `AnatomicalLandmarkCoordinates` field in the JSON sidecar of the corresponding
 T1w MRI anatomical data of the subject seen in the MEG session
-(see [Anatomy Imaging Data](01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)).
+(see [Anatomy Imaging Data](magnetic-resonance-imaging-data.md#anatomy-imaging-data)).
 
 For example: `"sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.json"`
 
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/modality-specific-files/microscopy.md
similarity index 95%
rename from src/04-modality-specific-files/10-microscopy.md
rename to src/modality-specific-files/microscopy.md
index 148b098850..de5bf08096 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/modality-specific-files/microscopy.md
@@ -1,9 +1,9 @@
 # Microscopy
 
 Support for Microscopy was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
 
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -58,7 +58,7 @@ Microscopy raw data MUST be stored in one of the following formats:
 -   [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)
 
 If different from PNG, TIFF, OME-TIFF, or OME-ZARR, the original unprocessed data in the native format MAY be
-stored in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data).
+stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data).
 
 ### Modality suffixes
 Microscopy data currently support the following imaging modalities:
@@ -126,7 +126,7 @@ A guide for using macros can be found at
 
 In this example, the JSON metadata is common for all samples of `sub-01`.
 JSON metadata may be defined per subject or per sample as appropriate, as per the
-[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+[inheritance principle](../common-principles.md#the-inheritance-principle).
 
 The [`acq-<label>`](../appendices/entities.md#acq) entity corresponds to a custom label that
 MAY be used to distinguish a different set of parameters used for acquiring the same modality.
@@ -224,11 +224,11 @@ A guide for using macros can be found at
 The index number can be assigned arbitrarily and, in the case of "ordered" chunks, the chunks'
 relative positions (in terms of scaling and translation) SHOULD be defined by an affine
 transformation matrix in the JSON sidecar file of each chunk, as described in
-[Chunk Transformations](10-microscopy.md#chunk-transformations).
+[Chunk Transformations](microscopy.md#chunk-transformations).
 
 In this example, the JSON metadata is different for each chunk of `sub-01_sample-01`.
 JSON metadata may be defined per sample or per chunk as appropriate, as per the
-[inheritance principle](../02-common-principles.md#the-inheritance-principle).
+[inheritance principle](../common-principles.md#the-inheritance-principle).
 
 In microscopy, many pyramidal file formats store multiple resolutions for the same acquisition.
 In the case where a multiple resolutions file format is converted to single resolution file format,
@@ -265,7 +265,7 @@ A guide for using macros can be found at
    }
 ) }}
 
-See [Preprocessed, coregistered and/or resampled volumes](../05-derivatives/03-imaging.md#preprocessed-coregistered-andor-resampled-volumes)
+See [Preprocessed, coregistered and/or resampled volumes](../derivatives/imaging.md#preprocessed-coregistered-andor-resampled-volumes)
 for details.
 
 ### Microscopy metadata (Sidecar JSON)
@@ -391,7 +391,7 @@ In this example, there is no scaling and `chunk-01` is at the origin.
 
 ## Required Samples file
 
-For Microscopy data, the [Samples file](../03-modality-agnostic-files.md#samples-file)
+For Microscopy data, the [Samples file](../modality-agnostic-files.md#samples-file)
 `samples.tsv` is REQUIRED and its associated sidecar `samples.json` file is RECOMMENDED.
 
 Additional optional columns MAY be used to describe other samples' attributes.
@@ -399,7 +399,7 @@ Additional optional columns MAY be used to describe other samples' attributes.
 ## Recommended Participants data
 
 For Microscopy data, we RECOMMEND to make use of the columns `species`, `strain` and
-`strain_rrid` in the [Participants file](../03-modality-agnostic-files.md#participants-file)
+`strain_rrid` in the [Participants file](../modality-agnostic-files.md#participants-file)
 when applicable.
 
 Additional optional columns MAY be used to describe other subjects' attributes.
diff --git a/src/04-modality-specific-files/11-near-infrared-spectroscopy.md b/src/modality-specific-files/near-infrared-spectroscopy.md
similarity index 97%
rename from src/04-modality-specific-files/11-near-infrared-spectroscopy.md
rename to src/modality-specific-files/near-infrared-spectroscopy.md
index 58605c44be..edfb075480 100644
--- a/src/04-modality-specific-files/11-near-infrared-spectroscopy.md
+++ b/src/modality-specific-files/near-infrared-spectroscopy.md
@@ -1,8 +1,8 @@
 # Near-Infrared Spectroscopy
 
 Support for Near-Infrared Spectroscopy (NIRS) was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -27,9 +27,9 @@ easily parsed by humans and machines that do not have a SNIRF reader at hand,
 which improves findability and tooling development.
 
 Raw NIRS data in the native format, if different from SNIRF, can also
-be stored in the [`/sourcedata`](../02-common-principles.md#source-vs-raw-vs-derived-data)
+be stored in the [`/sourcedata`](../common-principles.md#source-vs-raw-vs-derived-data)
 directory along with code to convert the data to
-SNIRF in the [`/code`](../02-common-principles.md#storage-of-derived-datasets) directory.
+SNIRF in the [`/code`](../common-principles.md#storage-of-derived-datasets) directory.
 The unprocessed raw data should be stored in
 the manufacturer's format before any additional processing or conversion is applied.
 Retaining the native file format is especially valuable in a case when conversion elicits the
@@ -71,7 +71,7 @@ and describes the positioning of the optodes.
 This field may also contain a reference to a file providing a graphical depiction of the cap,
 for example a PDF file, a photo, or a bitmap drawing.
 If the referred file is not specified in BIDS, it MAY be placed in the
-[`/sourcedata`](../02-common-principles.md#source-vs-raw-vs-derived-data) directory.
+[`/sourcedata`](../common-principles.md#source-vs-raw-vs-derived-data) directory.
 To clarify the usage and interaction of these fields, the following examples are provided:
 
 -   If a commercial cap such as EasyCap actiCAP 64 Ch Standard-2 was used:
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/modality-specific-files/physiological-and-other-continuous-recordings.md
similarity index 97%
rename from src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
rename to src/modality-specific-files/physiological-and-other-continuous-recordings.md
index b8384e851c..72ee2faefa 100644
--- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+++ b/src/modality-specific-files/physiological-and-other-continuous-recordings.md
@@ -62,7 +62,7 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table(["continuous.Continuous", "continuous.Physio"]) }}
 
 Additional metadata may be included as in
-[any TSV file](../02-common-principles.md#tabular-files) to specify, for
+[any TSV file](../common-principles.md#tabular-files) to specify, for
 example, the units of the recorded time series.
 Please note that, in contrast to other TSV files in BIDS, the TSV files specified
 for physiological and other continuous recordings *do not* include a header
@@ -136,7 +136,7 @@ and `Manufacturer`,
 each individual column in the TSV file may be documented as its own field in the JSON file
 (identical to the practice in other TSV+JSON file pairs).
 Here, only the `Description` and `Units` fields are shown, but you may use any other of the
-[defined fields](../02-common-principles.md#tabular-files) such as `TermURL`, `LongName`, and so on.
+[defined fields](../common-principles.md#tabular-files) such as `TermURL`, `LongName`, and so on.
 In this example, the `"cardiac"` and `"respiratory"` time series are produced by devices from
 the same manufacturer and follow the same sampling frequency.
 To specify different sampling frequencies or manufacturers, the time series would have to be split
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
similarity index 94%
rename from src/04-modality-specific-files/09-positron-emission-tomography.md
rename to src/modality-specific-files/positron-emission-tomography.md
index 5202926e94..2e704b6cb1 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -1,8 +1,8 @@
 # Positron Emission Tomography
 
 Support for Positron Emission Tomography (PET) was developed as a
-[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals).
-Please see [Citing BIDS](../01-introduction.md#citing-bids)
+[BIDS Extension Proposal](../extensions.md#bids-extension-proposals).
+Please see [Citing BIDS](../introduction.md#citing-bids)
 on how to appropriately credit this extension when referring to it in the
 context of the academic literature.
 
@@ -18,7 +18,7 @@ PET-BIDS is fully consistent with the BIDS specification as a whole.
 However, BIDS was initially developed in the context of MRI,
 so some terminology may be unfamiliar to researchers from each field.
 This section adds clarifications to
-[Common Principles - Definitions](../02-common-principles.md#definitions)
+[Common Principles - Definitions](../common-principles.md#definitions)
 for the PET context, and introduces the term "time zero" which is currently
 specific to PET.
 
@@ -81,7 +81,7 @@ Volumes MUST be stored in chronological order (the order they were acquired in).
 The OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used to
 indicate a task subjects were asked to perform in the scanner.
 Those labels MUST be consistent across subjects and sessions.
-For task based PET, a corresponding [`task events`](./05-task-events.md) file MUST be provided
+For task based PET, a corresponding [`task events`](./task-events.md) file MUST be provided
 (please note that this file is not necessary for resting scans).
 
 The [`trc-<label>`](../appendices/entities.md#trc) entity is used to
@@ -119,7 +119,7 @@ PET and MRI images may be aggregated in the same dataset.
 When analyzing MRI and PET data together,
 it is essential to specify whether MR images have been corrected for gradient non-linearities,
 using the `NonLinearGradientCorrection` metadata field
-(see [Sequence Specifics](./01-magnetic-resonance-imaging-data.md#sequence-specifics)),
+(see [Sequence Specifics](./magnetic-resonance-imaging-data.md#sequence-specifics)),
 which is REQUIRED for all MR data if PET data is also present in the dataset
 (see also [PET-MRI correspondence](../appendices/cross-modality-correspondence.md#pet-mri-correspondence)).
 In the case of studies using combined PET/fMRI,
@@ -127,7 +127,7 @@ subject-specific tasks may be carried out during the acquisition within the same
 If the same task is recorded with both modalities,
 the same [`task-<label>`](../appendices/entities.md#task) entity SHOULD be used.
 For further details, see
-[Task (including resting state) imaging data](./01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+[Task (including resting state) imaging data](./magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 In addition to the imaging data (`*.nii`) a `_pet.json` sidecar file MUST be provided.
 The included metadata are divided into sections described below.
@@ -187,7 +187,7 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("pet.PETTime") }}
 
-We refer to the common principles for the standards for describing dates and timestamps, including possibilities for anonymization (see [Units](../02-common-principles.md#units)).
+We refer to the common principles for the standards for describing dates and timestamps, including possibilities for anonymization (see [Units](../common-principles.md#units)).
 
 #### Reconstruction
 
@@ -269,8 +269,8 @@ Knudsen et al. 2020
 ([doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433))
 recommends recording participant body weight.
 If recorded once per participant, these data SHOULD be included in the
-[Participants file](../03-modality-agnostic-files.md#participants-file) or as
-[Phenotypic and assessment data](../03-modality-agnostic-files.md#phenotypic-and-assessment-data).
+[Participants file](../modality-agnostic-files.md#participants-file) or as
+[Phenotypic and assessment data](../modality-agnostic-files.md#phenotypic-and-assessment-data).
 
 For example:
 
@@ -282,7 +282,7 @@ sub-03 72
 ```
 
 If multiple measurements are made, these data SHOULD be included in the
-[Sessions file](../03-modality-agnostic-files.md#sessions-file).
+[Sessions file](../modality-agnostic-files.md#sessions-file).
 
 For example:
 
@@ -304,7 +304,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_filename_template("raw", datatypes=["pet"], suffixes=["blood"]) }}
 
 If collected, blood measurements of radioactivity are be stored in
-[Tabular files](../02-common-principles.md#tabular-files) and located in
+[Tabular files](../common-principles.md#tabular-files) and located in
 the `pet/` directory along with the corresponding PET data.
 
 The REQUIRED `recording` entity is used to distinguish sampling methods.
@@ -354,7 +354,7 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_columns_table("pet.Blood") }}
 
-As with all [tabular files](../02-common-principles.md#tabular-files),
+As with all [tabular files](../common-principles.md#tabular-files),
 additional columns MAY be defined in `_blood.json`.
 For clarity, it is RECOMMENDED to include the above column definitions in `_blood.json`,
 as shown in the following example.
diff --git a/src/04-modality-specific-files/05-task-events.md b/src/modality-specific-files/task-events.md
similarity index 97%
rename from src/04-modality-specific-files/05-task-events.md
rename to src/modality-specific-files/task-events.md
index 3332a78106..f15a708290 100644
--- a/src/04-modality-specific-files/05-task-events.md
+++ b/src/modality-specific-files/task-events.md
@@ -3,7 +3,7 @@
 The purpose of this file is to describe timing and other properties of events
 recorded during a run.
 Events are, for example, stimuli presented to the participant or participant responses
-(see [Definitions](../02-common-principles.md#definitions)).
+(see [Definitions](../common-principles.md#definitions)).
 A single event file MAY include any combination of stimulus, response, and other events.
 Events MAY overlap in time.
 Please mind that this does not imply that only so called "event related" study designs
@@ -26,10 +26,10 @@ Where `<matches>` corresponds to task filename. For example:
 Each task events file REQUIRES a corresponding task data file.
 It is also possible to have a single `events.tsv` file describing events
 for all participants and runs (see
-[Inheritance Principle](../02-common-principles.md#the-inheritance-principle)).
+[Inheritance Principle](../common-principles.md#the-inheritance-principle)).
 As with all other tabular data, `events.tsv` files MAY be accompanied by a JSON
 file describing the columns in detail (see
-[Tabular Files](../02-common-principles.md#tabular-files)).
+[Tabular Files](../common-principles.md#tabular-files)).
 
 The tabular files consists of one row per event and a set of REQUIRED
 and OPTIONAL columns:
diff --git a/src/pregh-changes.md b/src/pregh-changes.md
index da91e7f2e5..2cba2a81df 100644
--- a/src/pregh-changes.md
+++ b/src/pregh-changes.md
@@ -9,30 +9,30 @@
 
 -   Added support for MEG data (merged BEP008).
 -   Added `SequenceName` field.
--   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](04-modality-specific-files/05-task-events.md).
--   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](modality-specific-files/task-events.md).
+-   Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 -   Added `DwellTime` field.
 
 ## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18)
 
--   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for multiple defacing masks: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for multiple defacing masks: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added `DelayTime` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13)
 
--   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
--   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
+-   Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data).
 
 ## 1.0.1-rc1
 
--   Added T1 Rho maps: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data).
--   Added support for phenotypic information split into multiple files: [3.2 Participant key file](03-modality-agnostic-files.md#participants-file).
+-   Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data).
+-   Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file).
 -   Added recommendations for multi site datasets.
 -   Added `SoftwareVersions`.
 -   Added `run-<run_index>` to the phase encoding maps. Improved the description.
diff --git a/src/schema/README.md b/src/schema/README.md
index 23f8d6977e..335c56522f 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -85,13 +85,13 @@ Because the same description may be used in multiple locations, a mechanism is n
 to ensure that the correct path is discovered to render the description in each location.
 To do this, the path should follow the form `SPEC_ROOT/path/within/source.md#anchor`.
 For example, to link to the
-[Definitions](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#definitions)
+[Definitions](https://bids-specification.readthedocs.io/en/stable/common-principles.html#definitions)
 section of
-[Common principles](https://bids-specification.readthedocs.io/en/stable/02-common-principles.html),
-use the path `SPEC_ROOT/02-common-principles.md#definitions`:
+[Common principles](https://bids-specification.readthedocs.io/en/stable/common-principles.html),
+use the path `SPEC_ROOT/common-principles.md#definitions`:
 
 ```Markdown
-[Common principles - Definitions](SPEC_ROOT/02-common-principles.md#definitions)
+[Common principles - Definitions](SPEC_ROOT/common-principles.md#definitions)
 ```
 
 Note that the Markdown extension `.md` MUST be used for this to render correctly.
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 627786fe10..381ebd667a 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -20,7 +20,7 @@ acq_time__scans:
     Furthermore, if this header is provided, the acquisition times of all files
     from the same recording MUST be identical.
     Datetime format and their anonymization are described in
-    [Units](SPEC_ROOT/02-common-principles.md#units).
+    [Units](SPEC_ROOT/common-principles.md#units).
   type: string
   format: datetime
 acq_time__sessions:
@@ -29,7 +29,7 @@ acq_time__sessions:
   description: |
     Acquisition time refers to when the first data point of the first run was acquired.
     Datetime format and their anonymization are described in
-    [Units](SPEC_ROOT/02-common-principles.md#units).
+    [Units](SPEC_ROOT/common-principles.md#units).
   type: string
   format: datetime
 age:
@@ -749,7 +749,7 @@ units:
   description: |
     Physical unit of the value represented in this channel,
     for example, `V` for Volt, or `fT/cm` for femto Tesla per centimeter
-    (see [Units](SPEC_ROOT/02-common-principles.md#units)).
+    (see [Units](SPEC_ROOT/common-principles.md#units)).
   type: string
   format: unit
 units__nirs:
@@ -760,7 +760,7 @@ units__nirs:
     specified according to the SI unit symbol and possibly prefix symbol,
     or as a derived SI unit (for example, `V`, or unitless for changes in optical densities).
     For guidelines about units see the [Appendix](SPEC_ROOT/appendices/units.md)
-    and [Common Principles](SPEC_ROOT/02-common-principles.md#units) pages.
+    and [Common Principles](SPEC_ROOT/common-principles.md#units) pages.
   type: string
   format: unit
 value:
diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index a418b74004..87c0d16729 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -92,7 +92,7 @@ label:
     An alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent indentation,
     for example, it is `rest` in `task-rest` following `task-<label>` specification.
     Note that labels MUST not collide when casing is ignored
-    (see [Case collision intolerance](SPEC_ROOT/02-common-principles.md#case-collision-intolerance)).
+    (see [Case collision intolerance](SPEC_ROOT/common-principles.md#case-collision-intolerance)).
 modality:
   name: Modality
   display_name: Modality
@@ -113,10 +113,10 @@ run:
     or randomized nature of the stimuli).
     Run is a synonym of a data acquisition.
     Note that "uninterrupted" may look different by modality due to the nature of the recording.
-    For example, in [MRI](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md)
-    or [MEG](SPEC_ROOT/04-modality-specific-files/02-magnetoencephalography.md),
+    For example, in [MRI](SPEC_ROOT/modality-specific-files/magnetic-resonance-imaging-data.md)
+    or [MEG](SPEC_ROOT/modality-specific-files/magnetoencephalography.md),
     if a subject leaves the scanner, the acquisition must be restarted.
-    For some types of [PET](SPEC_ROOT/04-modality-specific-files/09-positron-emission-tomography.md) acquisitions,
+    For some types of [PET](SPEC_ROOT/modality-specific-files/positron-emission-tomography.md) acquisitions,
     a subject may leave and re-enter the scanner without interrupting the scan.
 sample:
   name: Sample
@@ -141,14 +141,14 @@ session:
     Defining multiple sessions is appropriate when several identical or similar data acquisitions
     are planned and performed on all -or most- subjects,
     often in the case of some intervention between sessions (for example, training).
-    In the [PET](SPEC_ROOT/04-modality-specific-files/09-positron-emission-tomography.md) context,
+    In the [PET](SPEC_ROOT/modality-specific-files/positron-emission-tomography.md) context,
     a session may also indicate a group of related scans, taken in one or more visits.
 suffix:
   name: suffix
   display_name: suffix
   description: |
     An alphanumeric string that forms part of a filename, located after all
-    [entities](SPEC_ROOT/02-common-principles.md#entities) and
+    [entities](SPEC_ROOT/common-principles.md#entities) and
     following a final `_`, right before the **file extension**;
     for example, it is `eeg` in `sub-05_task-matchingpennies_eeg.vhdr`.
 subject:
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 2f97f01c8b..4460c87e9e 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -340,7 +340,7 @@ split:
     If there are multiple parts of a recording and the optional `scans.tsv` is provided,
     all files MUST be listed separately in `scans.tsv` and
     the entries for the `acq_time` column in `scans.tsv` MUST all be identical,
-    as described in [Scans file](SPEC_ROOT/03-modality-agnostic-files.md#scans-file).
+    as described in [Scans file](SPEC_ROOT/modality-agnostic-files.md#scans-file).
   type: string
   format: index
 stain:
@@ -384,7 +384,7 @@ task:
     The `task-<label>` MUST be consistent across subjects and sessions.
 
     Files with the `task-<label>` entity SHOULD have an associated
-    [events file](SPEC_ROOT/04-modality-specific-files/05-task-events.md#task-events),
+    [events file](SPEC_ROOT/modality-specific-files/task-events.md#task-events),
     as well as certain metadata fields in the associated JSON file.
 
     For the purpose of this specification we consider the so-called "resting state" a task,
diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml
index b9501bab5c..1180509921 100644
--- a/src/schema/objects/files.yaml
+++ b/src/schema/objects/files.yaml
@@ -122,7 +122,7 @@ samples:
     -   `pathology`: string value describing the pathology of the sample or type of control.
         When different from `healthy`, pathology SHOULD be specified in `samples.tsv`.
         The pathology MAY instead be specified in
-        [Sessions files](SPEC_ROOT/03-modality-agnostic-files.md#sessions-file) in case it changes over time.
+        [Sessions files](SPEC_ROOT/modality-agnostic-files.md#sessions-file) in case it changes over time.
 
     -   `derived_from`: `sample-<label>` key/value pair from which a sample is derived from,
         for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`)
@@ -132,14 +132,14 @@ code:
   description: |
     A directory in which to store any code
     (for example the one used to generate the derivatives from the raw data).
-    See the [Code section](SPEC_ROOT/03-modality-agnostic-files.md#code)
+    See the [Code section](SPEC_ROOT/modality-agnostic-files.md#code)
     for more information.
 derivatives:
   display_name: Derivative data
   file_type: directory
   description: |
     Derivative data (for example preprocessed files).
-    See the [relevant section](SPEC_ROOT/02-common-principles.md#source-vs-raw-vs-derived-data)
+    See the [relevant section](SPEC_ROOT/common-principles.md#source-vs-raw-vs-derived-data)
     for more information.
 sourcedata:
   display_name: Source data
@@ -147,12 +147,12 @@ sourcedata:
   description: |
     A directory where to store data before harmonization, reconstruction,
     and/or file format conversion (for example, E-Prime event logs or DICOM files).
-    See the [relevant section](SPEC_ROOT/02-common-principles.md#source-vs-raw-vs-derived-data)
+    See the [relevant section](SPEC_ROOT/common-principles.md#source-vs-raw-vs-derived-data)
     for more information.
 stimuli:
   display_name: Stimulus files
   file_type: directory
   description: |
     A directory to store any stimulus files used during an experiment.
-    See the [relevant section](SPEC_ROOT/04-modality-specific-files/05-task-events.md#stimuli-directory)
+    See the [relevant section](SPEC_ROOT/modality-specific-files/task-events.md#stimuli-directory)
     for more information.
diff --git a/src/schema/objects/formats.yaml b/src/schema/objects/formats.yaml
index 9be89d5652..88d1bafbe5 100644
--- a/src/schema/objects/formats.yaml
+++ b/src/schema/objects/formats.yaml
@@ -118,7 +118,7 @@ unit:
   description: |
     A unit.
     SI units in CMIXF formatting are RECOMMENDED
-    (see [Units](SPEC_ROOT/02-common-principles.md#units)).
+    (see [Units](SPEC_ROOT/common-principles.md#units)).
 
     Currently this matches any string.
 
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 8d83d4cef8..a59a21b58c 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -154,10 +154,10 @@ AssociatedEmptyRoom:
   name: AssociatedEmptyRoom
   display_name: Associated Empty Room
   description: |
-    One or more [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri)
+    One or more [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri)
     pointing to empty-room file(s) associated with the subject's MEG recording.
     Using forward-slash separated paths relative to the dataset root is
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
   anyOf:
     - type: array
       items:
@@ -272,7 +272,7 @@ BasedOn:
     List of files in a file collection to generate the map.
     Fieldmaps are also listed, if involved in the processing.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the
-    `Sources` field using [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri)
+    `Sources` field using [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri)
     to distinguish sources from different datasets.
   anyOf:
     - type: string
@@ -304,7 +304,7 @@ BodyPartDetailsOntology:
   name: BodyPartDetailsOntology
   display_name: Body Part Details Ontology
   description: |
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator) of ontology used for
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator) of ontology used for
     BodyPartDetails (for example: `"https://www.ebi.ac.uk/ols/ontologies/uberon"`).
   type: string
   format: uri
@@ -431,7 +431,7 @@ Code:
   name: Code
   display_name: Code
   description: |
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
     of the code used to present the stimuli.
     Persistent identifiers such as DOIs are preferred.
     If multiple versions of code may be hosted at the same location,
@@ -442,7 +442,7 @@ CogAtlasID:
   name: CogAtlasID
   display_name: Cognitive Atlas ID
   description: |
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
     of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/)
     Task term.
   type: string
@@ -451,7 +451,7 @@ CogPOID:
   name: CogPOID
   display_name: Cognitive Paradigm Ontology ID
   description: |
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
     of the corresponding [CogPO](http://www.cogpo.org/) term.
   type: string
   format: uri
@@ -507,16 +507,16 @@ DatasetDOI:
   description: |
     The Digital Object Identifier of the dataset (not the corresponding paper).
     DOIs SHOULD be expressed as a valid
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator);
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator);
     bare DOIs such as `10.0.2.3/dfjj.10` are
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
   type: string
   format: uri
 DatasetLinks:
   name: DatasetLinks
   display_name: Dataset Links
   description: |
-    Used to map a given `<dataset-name>` from a [BIDS URI](SPEC_ROOT/02-common-principles.md#bids-uri)
+    Used to map a given `<dataset-name>` from a [BIDS URI](SPEC_ROOT/common-principles.md#bids-uri)
     of the form `bids:<dataset-name>:path/within/dataset` to a local or remote location.
     The `<dataset-name>`: `""` (an empty string) is a reserved keyword that MUST NOT be a key in
     `DatasetLinks` (example: `bids::path/within/dataset`).
@@ -831,7 +831,7 @@ EchoTime:
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation
     of the data, such as in
-    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#\
+    [ASL](SPEC_ROOT/modality-specific-files/magnetic-resonance-imaging-data.md#\
     arterial-spin-labeling-perfusion-data)
     or variable echo time fMRI sequences.
   anyOf:
@@ -1024,7 +1024,7 @@ FlipAngle:
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation of
     the data, such as in
-    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#\
+    [ASL](SPEC_ROOT/modality-specific-files/magnetic-resonance-imaging-data.md#\
     arterial-spin-labeling-perfusion-data)
     or variable flip angle fMRI sequences.
   anyOf:
@@ -1117,14 +1117,14 @@ Genetics:
     Database:
       name: Database
       description: |
-        [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+        [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
         of database where the dataset is hosted.
       type: string
       format: uri
     Dataset:
       name: Dataset
       description: |
-        [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+        [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
         where data can be retrieved.
       type: string
       format: uri
@@ -1133,7 +1133,7 @@ Genetics:
       description: |
         List of relevant descriptors (for example, journal articles) for dataset
         using a valid
-        [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+        [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
         when possible.
       anyOf:
         - type: string
@@ -1304,7 +1304,7 @@ ImageAcquisitionProtocol:
   display_name: Image Acquisition Protocol
   description: |
     Description of the image acquisition protocol or
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
     (for example from [protocols.io](https://www.protocols.io/)).
   type: string
 ImageDecayCorrected:
@@ -1473,9 +1473,9 @@ IntendedFor:
   display_name: Intended For
   description: |
     The paths to files for which the associated file is intended to be used.
-    Contains one or more [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri).
+    Contains one or more [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri).
     Using forward-slash separated paths relative to the participant subdirectory is
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
   anyOf:
     - type: string
       format: bids_uri
@@ -1493,9 +1493,9 @@ IntendedFor__ds_relative:
   display_name: Intended For
   description: |
     The paths to files for which the associated file is intended to be used.
-    Contains one or more [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri).
+    Contains one or more [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri).
     Using forward-slash separated paths relative to the dataset root is
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
   anyOf:
     - type: string
       format: bids_uri
@@ -2416,7 +2416,7 @@ RawSources:
     A list of paths relative to dataset root pointing to the BIDS-Raw file(s)
     that were used in the creation of this derivative.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the
-    `Sources` field using [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri)
+    `Sources` field using [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri)
     to distinguish sources from different datasets.
   type: array
   items:
@@ -2524,7 +2524,7 @@ ReferencesAndLinks:
   description: |
     List of references to publications that contain information on the dataset.
     A reference may be textual or a
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator).
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator).
   items:
     type: string
   type: array
@@ -2565,7 +2565,7 @@ RepetitionTimeExcitation:
     `"RepetitionTimePreparation"` if needed) for anatomy imaging data rather than
     `"RepetitionTime"` as it is already defined as the amount of time that it takes
     to acquire a single volume in the
-    [task imaging data](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-\
+    [task imaging data](SPEC_ROOT/modality-specific-files/magnetic-resonance-\
     imaging-data.md#task-including-resting-state-imaging-data)
     section.
   type: number
@@ -2583,7 +2583,7 @@ RepetitionTimePreparation:
     The data type array provides a value for each volume in a 4D dataset and
     should only be used when the volume timing is critical for interpretation of
     the data, such as in
-    [ASL](SPEC_ROOT/04-modality-specific-files/01-magnetic-resonance-imaging-data.md\
+    [ASL](SPEC_ROOT/modality-specific-files/magnetic-resonance-imaging-data.md\
     #arterial-spin-labeling-perfusion-data).
   anyOf:
     - type: number
@@ -2642,7 +2642,7 @@ SampleExtractionProtocol:
   display_name: Sample Extraction Protocol
   description: |
     Description of the sample extraction protocol or
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
     (for example from [protocols.io](https://www.protocols.io/)).
   type: string
 SampleFixation:
@@ -2747,7 +2747,7 @@ ScanDate:
   description: |
     Date of scan in the format `"YYYY-MM-DD[Z]"`.
     This field is DEPRECATED, and this metadata SHOULD be recorded in the `acq_time` column of the
-    corresponding [Scans file](SPEC_ROOT/03-modality-agnostic-files.md#scans-file).
+    corresponding [Scans file](SPEC_ROOT/modality-agnostic-files.md#scans-file).
   type: string
   format: date
 ScanOptions:
@@ -2935,7 +2935,7 @@ SourceDatasets:
   description: |
     Used to specify the locations and relevant attributes of all source datasets.
     Valid keys in each object include `"URL"`, `"DOI"` (see
-    [URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)), and
+    [URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)), and
     `"Version"` with
     [string](https://www.w3schools.com/js/js_json_datatypes.asp)
     values.
@@ -2955,7 +2955,7 @@ Sources:
   display_name: Sources
   description: |
     A list of files with the paths specified using
-    [BIDS URIs](SPEC_ROOT/02-common-principles.md#bids-uri);
+    [BIDS URIs](SPEC_ROOT/common-principles.md#bids-uri);
     these files were directly used in the creation of this derivative data file.
     For example, if a derivative A is used in the creation of another
     derivative B, which is in turn used to generate C in a chain of A->B->C,
@@ -2964,7 +2964,7 @@ Sources:
     then Z should list X and Y in `"Sources"`,
     regardless of whether X was used to generate Y.
     Using paths specified relative to the dataset root is
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
   type: array
   items:
     type: string
@@ -3279,7 +3279,7 @@ Units:
   description: |
     Measurement units for the associated file.
     SI units in CMIXF formatting are RECOMMENDED
-    (see [Units](SPEC_ROOT/02-common-principles.md#units)).
+    (see [Units](SPEC_ROOT/common-principles.md#units)).
   type: string
   format: unit
 VascularCrushing:
@@ -3454,7 +3454,7 @@ iEEGCoordinateSystem:
     (of either a volume-rendering, surface-rendering, operative photo, or
     operative drawing), this MUST be `"Pixels"`.
     For more information, see the section on
-    [2D coordinate systems](SPEC_ROOT/04-modality-specific-files/04-intracranial\
+    [2D coordinate systems](SPEC_ROOT/modality-specific-files/intracranial\
     -electroencephalography.md#allowed-2d-coordinate-systems).
   anyOf:
     - $ref: objects.metadata._iEEGCoordSys
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 4c376d45ca..9e5a41b966 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -528,7 +528,7 @@ blood:
   display_name: Blood recording data
   description: |
     Blood measurements of radioactivity stored in
-    [tabular files](SPEC_ROOT/02-common-principles.md#tabular-files)
+    [tabular files](SPEC_ROOT/common-principles.md#tabular-files)
     and located in the `pet/` directory along with the corresponding PET data.
 bold:
   value: bold
@@ -691,7 +691,7 @@ phase:
   value: phase
   display_name: Phase image
   description: |
-    [DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions).
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
     Phase information associated with magnitude information stored in BOLD
     contrast.
     This suffix should be replaced by the
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index c5abb23c85..41dae7a40f 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -128,7 +128,7 @@ MEGCoordsystemWithEEG:
       level: optional
       description_addendum: |
         See [Recording EEG simultaneously with MEG]
-        (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
         Preferably the same as the `MEGCoordinateSystem`.
     EEGCoordinateUnits: optional
     EEGCoordinateSystemDescription:
@@ -136,7 +136,7 @@ MEGCoordsystemWithEEG:
       level_addendum: required if `EEGCoordinateSystem` is `Other`
       description_addendum: |
         See [Recording EEG simultaneously with MEG]
-        (/04-modality-specific-files/02-magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
+        (/modality-specific-files/magnetoencephalography.html#recording-eeg-simultaneously-with-meg).
 
 # NOTE: The JSON isn't really a sidecar, so "sidecar.MEGCoordinateSystem" is misleading.
 MEGCoordsystemWithEEGMEGCoordinateSystem:
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index e07a514ff0..d968d48c51 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -54,7 +54,7 @@ MRISequenceSpecifics:
     SequenceName: recommended
     PulseSequenceDetails: recommended
     NonlinearGradientCorrection: |
-      recommended, but required if [PET](./09-positron-emission-tomography.md) data are present
+      recommended, but required if [PET](./positron-emission-tomography.md) data are present
     MRAcquisitionType: recommended, but required for Arterial Spin Labeling
     MTState: recommended
     MTOffsetFrequency: optional
diff --git a/tools/schemacode/bidsschematools/render/tables.py b/tools/schemacode/bidsschematools/render/tables.py
index cc607cca16..59f00c8603 100644
--- a/tools/schemacode/bidsschematools/render/tables.py
+++ b/tools/schemacode/bidsschematools/render/tables.py
@@ -85,7 +85,7 @@ def _make_object_table(
         requirement_info = utils.normalize_requirements(requirement_info)
         requirement_info = requirement_info.replace(
             "DEPRECATED",
-            "[DEPRECATED](SPEC_ROOT/02-common-principles.md#definitions)",
+            "[DEPRECATED](SPEC_ROOT/common-principles.md#definitions)",
         )
 
         type_string = utils.resolve_metadata_type(subschema[element])