[CLN] Refactor sysdb and log service (#2893)

## Description of changes

*Summarize the changes made by this PR.*
 - This PR cleans out the sysdb and needless abstractions.
 - It removes the notification processor, and notifier since they are not used and don't intend to be used in the future
 - It removes the interfaces for the catalog and the coordinator since there is only one implementation and there's no future plans of having multiple implementations
 - It changes the directory structure to locate all the sysdb code together and similarly all the log service code together.
 - The directory structure has one directory per abstraction layer. Data models that interface two layer are present in the directory of the lower layer because the higher layer is technically dependent on the lower layer

## Test plan
- [x] Tests pass locally with `pytest` for python, `yarn test` for js, `cargo test` for rust

## Documentation Changes
None

go/Dockerfile.migration

@@ -5,9 +5,9 @@ RUN apt upgrade -y
 RUN apt install -y curl jq
 RUN curl -sSf https://atlasgo.sh | sh -s -- --community
 
-COPY ./go/migrations migrations
-COPY ./go/atlas.hcl atlas.hcl
+COPY ./go/pkg/sysdb/metastore/db/migrations migrations
+COPY ./go/pkg/sysdb/metastore/db/atlas.hcl atlas.hcl
 
 FROM arigaio/atlas:latest as logservice-migration
-COPY ./go/database/log/migrations migrations
-COPY ./go/database/log/atlas.hcl atlas.hcl
+COPY ./go/pkg/log/store/migrations migrations
+COPY ./go/pkg/log/store/atlas.hcl atlas.hcl

go/Makefile

@@ -18,7 +18,7 @@ docker:
 	docker build -t chroma-coordinator:latest .
 
 ### LOG SERVICE
-DATABABASE_LOG_DIR := database/log
+DATABABASE_LOG_DIR := pkg/log/store
 
 log_db_clean:
 	rm -rf $(DATABABASE_LOG_DIR)/db

go/cmd/coordinator/cmd.go

@@ -4,8 +4,8 @@ import (
 	"io"
 	"time"
 
-	"github.com/chroma-core/chroma/go/pkg/coordinator/grpc"
 	"github.com/chroma-core/chroma/go/pkg/grpcutils"
+	"github.com/chroma-core/chroma/go/pkg/sysdb/grpc"
 
 	"github.com/chroma-core/chroma/go/cmd/flag"
 	"github.com/chroma-core/chroma/go/pkg/utils"
@@ -41,11 +41,6 @@ func init() {
 	Cmd.Flags().IntVar(&conf.DBConfig.MaxOpenConns, "max-open-conns", 10, "MetaTable max open connections")
 	Cmd.Flags().StringVar(&conf.DBConfig.SslMode, "ssl-mode", "disable", "SSL mode for database connection")
 
-	// Notification
-	Cmd.Flags().StringVar(&conf.NotificationStoreProvider, "notification-store-provider", "memory", "Notification store provider")
-	Cmd.Flags().StringVar(&conf.NotifierProvider, "notifier-provider", "memory", "Notifier provider")
-	Cmd.Flags().StringVar(&conf.NotificationTopic, "notification-topic", "chroma-notification", "Notification topic")
-
 	// Memberlist
 	Cmd.Flags().StringVar(&conf.KubernetesNamespace, "kubernetes-namespace", "chroma", "Kubernetes namespace")
 	Cmd.Flags().DurationVar(&conf.ReconcileInterval, "reconcile-interval", 100*time.Millisecond, "Reconcile interval")