[ENH] Update standards section (#534)

* rm bids stats model * rm bids apps spec * rm bids apps spec * update index * update spec * clean up * update makefile * lint * test * fixes * fix * fix
bids-standard · Oct 18, 2024 · 217b135 · 217b135
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diff --git a/.github/workflows/check_md_links.yml b/.github/workflows/check_md_links.yml
@@ -13,8 +13,8 @@ jobs:
         -   uses: actions/checkout@master
         -   uses: gaurav-nelson/github-action-markdown-link-check@v1
             with:
-                use-quiet-mode: no
-                use-verbose-mode: no
+                use-quiet-mode: yes
+                # use-verbose-mode: no
                 config-file: md_link_check_config.json
                 folder-path: docs
                 file-path: ./README.md
diff --git a/.gitmodules b/.gitmodules
@@ -1,18 +1,6 @@
 [submodule "specification"]
 	path = specification
 	url = https://github.com/bids-standard/bids-specification.git
-[submodule "execution-spec"]
-	path = execution-spec
-	url = https://github.com/bids-standard/execution-spec
-	datalad-url = https://github.com/bids-standard/execution-spec
-[submodule "docs/standards/bids_stats_model/variable-transform"]
-	path = docs/standards/bids_stats_model/variable-transform
-	url = https://github.com/bids-standard/variable-transform.git
-	datalad-url = https://github.com/bids-standard/variable-transform.git
-[submodule "docs/standards/bids_stats_model/src"]
-	path = docs/standards/bids_stats_model/src
-	url = https://github.com/bids-standard/stats-models
-	datalad-url = https://github.com/bids-standard/stats-models
 [submodule "data/datasets/examples"]
 	path = data/datasets/examples
 	url = https://github.com/bids-standard/bids-examples

diff --git a/.remarkignore b/.remarkignore
@@ -1,5 +1,4 @@
 docs/collaboration/bids_github/
 docs/datasets/index.md
 docs/getting_started/folders_and_files/files.md
-docs/standards/bids_stats_model/src
-docs/standards/bids_stats_model/variable-transform
+docs/specification/macros_doc.md
diff --git a/docs/collaboration/bids_github b/docs/collaboration/bids_github
diff --git a/docs/collaboration/contributors.md b/docs/collaboration/contributors.md
diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md
@@ -222,7 +222,7 @@ they should inform the steering group in advance and are responsible to help:
 
 {{ MACROS___generate_members_table(file="advisory.yml") }}
 
-### Other working/interest Groups
+### Other working groups
 
 A working/interest group can be established under the approval of the BIDS Steering Group.
 This is typically but not limited to being formed for the purpose of advancing the BIDS community, not the standard.
@@ -486,8 +486,7 @@ Anonymous data from BIDS elections is stored in a dedicated repository on GitHub
 
 ### H. Governance amendment procedure
 
-A group of BIDS contributors may at any time form a [working
-group](#other-workinginterest-groups) to propose amendments to the governance.
+A group of BIDS contributors may at any time form a [working group](#other-working-groups) to propose amendments to the governance.
 These amendments will be first reviewed by the Steering Group before being
 submitted to a community review.
 At the end of the community review each amendment is submitted to a vote of BIDS

diff --git a/docs/collaboration/working-groups.md b/docs/collaboration/working-groups.md
@@ -8,7 +8,7 @@ to improve the documentation around BIDS...
 
 ## Forming a working group
 
-The rules to form a working group are mentioned in the [governance](./governance.md#other-workinginterest-groups).
+The rules to form a working group are mentioned in the [governance](./governance.md#other-working-groups).
 
 A template for the open-letter can be found in [this google doc](https://docs.google.com/document/d/1JfTliUcpyRAGdiZSHObkvZFdkrxPTclQTvolr8ssNHM/edit).
 

diff --git a/docs/standards/bids_app_specification/contributors.md b/docs/standards/bids_app_specification/contributors.md
diff --git a/docs/standards/bids_app_specification/index.md b/docs/standards/bids_app_specification/index.md
@@ -1,13 +1,8 @@
-# BIDS Apps execution specification
-
-## The Problem
-
-Neuroimaging is a field with an enormous library of powerful tools
-and openly available datasets that can be difficult to get to work together.
-
-## Why do we need the BIDS Application Specification?
+# BIDS Apps
 
 While BIDS is great for standardizing datasets, analytical tools can take a variety of forms, arguments,
 and complexities, limiting their ability to be applied interchangeably.
 The BIDS Application Specification solves this problem
 by creating a community-driven standardized structure for software definitions and their execution.
+
+The specification for the BIDS apps can be [browsed online](https://bids-standard.github.io/execution-spec/).
diff --git a/docs/standards/bids_app_specification/scope.md b/docs/standards/bids_app_specification/scope.md
diff --git a/docs/standards/bids_app_specification/specification/examples.md b/docs/standards/bids_app_specification/specification/examples.md
diff --git a/docs/standards/bids_app_specification/specification/index.md b/docs/standards/bids_app_specification/specification/index.md