Reorganized the directory structure of tools (#532)

* Added get_definitions to BaseInput

* Wrote tests for onset_manager creation

* Started work on the condition manager

* Partial implementation of condition_manager

* Updated the condition variable manager -- still incomplete

* Updated the variable manager before changes levels

* Updated the variable summary function

* Updated requirements to use >=

* Updated the docs -- still failing to generate all docs files

* Restored also_gather_defs

* Updated the HED factorization

* Reorganized the variable manager and variable summary

* Updated the api documentation

* Updated the filter concept

* Cleaned up the unit tests for the variable manager

* Updated the variable manager

* Got the unittests to run again

* Minor updates to assemlby

* Added exclude_dirs option to get_dir_dictionary

* Updated Bids File Summary to not require entitites

* Updated the init for some utilities

* Moved the util directory under tools