diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 5fdacec40b..fa9d6566cf 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -5,7 +5,7 @@ See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/
 - Please keep the title of your Pull Request (PR) short but informative - it will
   appear in the changelog.
 - If you do **not** want a PR to appear in the changelog, it must receive the `exclude-from-changelog` label.
-- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
   To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors) and add your name with the type of contribution.
   For assistance, please tag @bids-standard/maintainers.
 - Use one of the following prefixes in the title of your PR:
diff --git a/CODEOWNERS b/CODEOWNERS
index 6fd6504405..ec56a06da0 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -17,7 +17,7 @@
 /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/99-appendices/06-meg-file-formats.md @monkeyman192
+/src/appendices/meg-file-formats.md @monkeyman192
 
 # The schema
 /src/schema/ @tsalo @erdalkaraca
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7c7d6a4276..e04c237497 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -708,11 +708,11 @@ BIDS follows the
 specification, so we welcome and recognize all contributions from documentation
 to testing to code development.
 You can see a list of current contributors in the
-[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
 
 If you have made any type of contributions to the BIDS specifications, you can
 either make a change to the
-[contributors document](./src/99-appendices/01-contributors.md) and commit as
+[contributors document](./src/appendices/contributors.md) and commit as
 part of a pull request or you can edit this
 [page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors)
 of the specification WIKI.
diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index 9ea0706275..8ad8bbdb8d 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -61,7 +61,7 @@ Leaders of BIDS Extension Proposals are listed in the
 
 ### Contributors Group
 
-Contributors are listed in [Appendix I](https://bids-specification.readthedocs.io/en/stable/99-appendices/01-contributors.html)
+Contributors are listed in the [Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html)
 of the BIDS specification. Contributors who have not yet entered their name
 into this list are encouraged to edit the [Contributors WIKI page](https://github.com/bids-standard/bids-specification/wiki/Contributors)
 with their name, using the emojis listed in the WIKI to indicate their
diff --git a/README.md b/README.md
index 5bf0f2b55b..aefe81c848 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ The specification is provided in the form of a webpage, built using
 BIDS is a community-driven standard, and it depends on contributions from its members.
 We welcome new contributors, and we appreciate all contributions to the project!
 
-For a current list of our contributors, please see our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md).
+For a current list of our contributors, please see our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
 
 When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md).
 
diff --git a/Release_Protocol.md b/Release_Protocol.md
index 1a2cf9e973..67d34e4c98 100644
--- a/Release_Protocol.md
+++ b/Release_Protocol.md
@@ -66,7 +66,7 @@ Additionally, implement the same change in the version name perform above in the
 
 Note: this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. It will be generated once the GitHub release has been completed.
 
-Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/99-appendices/01-contributors.md)
+Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md)
 with the [Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Contributors)
 to ensure all contributors are duly credited.
 Be sure not to remove credits if both have been edited.
@@ -92,7 +92,7 @@ By pushing `rel/` branches to the main repository, the chances of continuous int
 discrepancies is reduced.
 
 ```Shell
-$ git add src/CHANGES.md mkdocs.yml src/99-appendices/01-contributors.md
+$ git add src/CHANGES.md mkdocs.yml src/appendices/contributors.md
 $ git commit -m 'REL: v1.2.0'
 $ git push -u upstream rel/1.2.0
 ```
diff --git a/mkdocs.yml b/mkdocs.yml
index 01eb96dd5c..1c2690b88b 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -31,6 +31,22 @@ plugins:
              - css/watermark.css
     - macros:
         module_name: tools/mkdocs_macros_bids/main
+    - redirects:
+        redirect_maps:
+            '99-appendices/14-glossary.md': 'glossary.md'
+            '99-appendices/01-contributors.md': 'appendices/contributors.md'
+            '99-appendices/02-licenses.md': 'appendices/licenses.md'
+            '99-appendices/03-hed.md': 'appendices/hed.md'
+            '99-appendices/04-entity-table.md': 'appendices/entity-table.md'
+            '99-appendices/05-units.md': 'appendices/units.md'
+            '99-appendices/06-meg-file-formats.md': 'appendices/meg-file-formats.md'
+            '99-appendices/07-meg-systems.md': 'appendices/meg-systems.md'
+            '99-appendices/08-coordinate-systems.md': 'appendices/coordinate-systems.md'
+            '99-appendices/09-entities.md': 'appendices/entities.md'
+            '99-appendices/10-file-collections.md': 'appendices/file-collections.md'
+            '99-appendices/11-qmri.md': 'appendices/qmri.md'
+            '99-appendices/12-arterial-spin-labeling.md': 'appendices/arterial-spin-labeling.md'
+            '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md'
 docs_dir: 'src'
 use_directory_urls: false
 nav:
@@ -54,22 +70,22 @@ nav:
         - 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: 99-appendices/01-contributors.md
-        - Licenses: 99-appendices/02-licenses.md
-        - Hierarchical Event Descriptors: 99-appendices/03-hed.md
-        - Entity table: 99-appendices/04-entity-table.md
-        - Units: 99-appendices/05-units.md
-        - MEG file formats: 99-appendices/06-meg-file-formats.md
-        - MEG systems: 99-appendices/07-meg-systems.md
-        - Coordinate systems: 99-appendices/08-coordinate-systems.md
-        - Entities: 99-appendices/09-entities.md
-        - File collections: 99-appendices/10-file-collections.md
-        - Quantitative MRI: 99-appendices/11-qmri.md
-        - Arterial Spin Labeling: 99-appendices/12-arterial-spin-labeling.md
-        - Cross modality correspondence: 99-appendices/13-cross-modality-correspondence.md
-        - Glossary: 99-appendices/14-glossary.md
+        - 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
diff --git a/pdf_build_src/pandoc_script.py b/pdf_build_src/pandoc_script.py
index 25d1a5e325..be7d399cee 100644
--- a/pdf_build_src/pandoc_script.py
+++ b/pdf_build_src/pandoc_script.py
@@ -50,11 +50,11 @@ def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"):
 
     # Resources are searched relative to the working directory, but
     # we can add additional search paths using <path>:<another path>, ...
-    # When in one of the 99-appendices/ files there is a reference to
+    # When in one of the appendices/ files there is a reference to
     # "../04-modality-specific-files/images/...", then we need to use
-    # 99-appendices/ as a resource-path so that the relative files can
+    # appendices/ as a resource-path so that the relative files can
     # be found.
-    cmd += [f'--resource-path=.:{str(root / "99-appendices")}']
+    cmd += [f'--resource-path=.:{str(root / "appendices")}']
 
     # Add input files to command
     # The filenames in `markdown_list` will ensure correct order when sorted
diff --git a/requirements.txt b/requirements.txt
index bb7bc004e9..25f0520a6a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,5 +3,6 @@ mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3
 mkdocs-macros-plugin
+mkdocs-redirects
 numpy
 tools/schemacode/[render]
diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 6553a56229..4844c1415e 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -56,11 +56,10 @@ entity instance, may be referred to as simply an "entity".
 "Subject", "session", "sample", "task", and "run" from the list of definitions
 above are all examples of entities.
 The comprehensive list of supported entities is defined in
-[Appendix IX](99-appendices/09-entities.md);
+the [Entities Appendix](appendices/entities.md);
 further, whether each is OPTIONAL, REQUIRED, or MUST NOT be provided for
 various data files, as well as their relative ordering in a filename, are
-defined in the Entity Table in
-[Appendix IV](99-appendices/04-entity-table.md).
+defined in the [Entity Tables Appendix](appendices/entity-table.md).
 
 ## Compulsory, optional, and additional data and metadata
 
@@ -134,12 +133,12 @@ In cases where an entity and a metadata field convey similar contextual
 information, the presence of an entity should not be used as a replacement for
 the corresponding metadata field.
 For instance, in echo-planar imaging MRI, the
-[`dir-<label>`](./99-appendices/09-entities.md#dir) entity MAY be used
+[`dir-<label>`](./appendices/entities.md#dir) entity MAY be used
 to distinguish files with different phase-encoding directions,
 but the file's `PhaseEncodingDirection` MUST be specified as metadata.
 
 A summary of all entities in BIDS and the order in which they MUST be
-specified is available in the [entity table](./99-appendices/04-entity-table.md)
+specified is available in the [entity table](./appendices/entity-table.md)
 in the appendix.
 
 ### Entity-linked file collections
@@ -161,7 +160,7 @@ Provided the conditions above are satisfied,
 any suffix (such as `bold`) can identify an entity-linked file collection,
 although certain suffixes are exclusive for this purpose (for example, `MP2RAGE`).
 Use cases concerning this convention are compiled in the
-[file collections](./99-appendices/10-file-collections.md) appendix.
+[file collections](./appendices/file-collections.md) appendix.
 This convention is mainly intended for but not limited to MRI modalities.
 
 ### Case collision intolerance
@@ -805,14 +804,14 @@ In case data is expressed in SI units or SI derived units, the units MAY be
 specified in the sidecar JSON file.
 In case non-standard prefixes are added to SI or non-SI units, these
 non-standard prefixed units MUST be specified in the JSON file.
-See [Appendix V](99-appendices/05-units.md) for a list of standard units and
+See the [Units Appendix](appendices/units.md) for a list of standard units and
 prefixes.
 Note also that for the *formatting* of SI units, the [CMIXF-12](https://people.csail.mit.edu/jaffer/MIXF/CMIXF-12)
 convention for encoding units is RECOMMENDED.
 CMIXF provides a consistent system for all units and prefix symbols with only basic
 characters, avoiding symbols that can cause text encoding problems; for example the
 CMIXF formatting for "micro volts" is `uV`, "degrees Celsius" is `oC` and "Ohm" is `Ohm`.
-See [Appendix V](99-appendices/05-units.md) for more information.
+See the [Units Appendix](appendices/units.md) for more information.
 
 For additional rules, see below:
 
@@ -866,7 +865,7 @@ Describing dates and timestamps:
     Some analysis software packages (for example, MNE-Python) handle their data as `.fif`
     internally and will break if recording dates are specified prior to `1902`,
     even if the original data format is not `.fif`.
-    See [MEG-file-formats](./99-appendices/06-meg-file-formats.md#recording-dates-in-fif-files)
+    See the [MEG File Formats Appendix](./appendices/meg-file-formats.md#recording-dates-in-fif-files)
     for more information.
 
 -   Age SHOULD be given as the number of years since birth at the time of
diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 381c297bec..18d331fd77 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -469,7 +469,7 @@ commonly used for qMRI,
 where recordings may be linked through entities such as `echo` and `part`
 (using `.nii` or `.nii.gz` extensions).
 For another example consider the case of large files in `.fif` format that are linked through the `split` entity
-(see [Split files](./99-appendices/06-meg-file-formats.md#split-files)).
+(see [Split files](./appendices/meg-file-formats.md#split-files)).
 Such recordings MUST be documented with one row per file
 (unlike the case of multi-file file formats described above).
 
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index d0a7d23af4..832d0d9b32 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -202,7 +202,7 @@ and a guide for using macros can be found at
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one MAY provide the binary mask that was used to
 remove facial features in the form of `_defacemask` files.
-In such cases,  the OPTIONAL [`mod-<label>`](../99-appendices/09-entities.md#mod)
+In such cases, the OPTIONAL [`mod-<label>`](../appendices/entities.md#mod)
 entity corresponds to modality suffix,
 such as `T1w` or `inplaneT1`, referenced by the defacemask image.
 For example, `sub-01_mod-T1w_defacemask.nii.gz`.
@@ -222,7 +222,7 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("anat.MRIAnatomyCommonMetadataFields") }}
 
-The [`part-<label>`](../99-appendices/09-entities.md#part) entity is
+The [`part-<label>`](../appendices/entities.md#part) entity is
 used to indicate which component of the complex representation of the MRI
 signal is represented in voxel data.
 This entity is associated with the DICOM Tag `0008, 9208`.
@@ -262,7 +262,7 @@ For example, for `sub-01_part-phase_T1w.json`:
 
 When there is only a magnitude image of a given type, the `part` entity MAY be omitted.
 
-Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
+Similarly, the OPTIONAL [`rec-<label>`](../appendices/entities.md#rec)
 entity can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
@@ -302,13 +302,13 @@ 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).
-Please visit the [file collections appendix](../99-appendices/10-file-collections.md) to see the
+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.
 For any other details on the organization of parametric maps, their
 recommended metadata fields, and the application specific entity or
-metadata requirement levels of [file collections](../99-appendices/10-file-collections.md) that can generate
-them, visit the [qMRI appendix](../99-appendices/11-qmri.md).
+metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate
+them, visit the [qMRI appendix](../appendices/qmri.md).
 
 ### Deprecated suffixes
 
@@ -374,7 +374,7 @@ For multiband acquisitions, one MAY also save the single-band reference image wi
 (for example, `sub-control01_task-nback_sbref.nii.gz`).
 
 Multi-echo data MUST be split into one file per echo using the
-[`echo-<index>`](../99-appendices/09-entities.md#echo) entity. For example:
+[`echo-<index>`](../appendices/entities.md#echo) entity. For example:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -574,7 +574,7 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_filename_template(datatypes=["dwi"]) }}
 
-The [`run-<index>`](../99-appendices/09-entities.md#run) entity is RECOMMENDED
+The [`run-<index>`](../appendices/entities.md#run) entity is RECOMMENDED
 to encode the splits of multipart DWI scans
 (see [below](#multipart-split-dwi-schemes) for more information on multipart DWI schemes).
 
@@ -617,7 +617,7 @@ volumes.
 Following the FSL format for the `[*_]dwi.bvec` specification, the coordinate system of
 the *b* vectors MUST be defined with respect to the coordinate system defined by
 the header of the corresponding `_dwi` NIfTI file and not the scanner's device
-coordinate system (see [Coordinate systems](../99-appendices/08-coordinate-systems.md)).
+coordinate system (see [Coordinate systems](../appendices/coordinate-systems.md)).
 The most relevant limitation imposed by this choice is that the gradient information cannot
 be directly stored in this format if the scanner generates *b*-vectors in *scanner coordinates*.
 
@@ -732,7 +732,7 @@ A guide for using macros can be found at
 ) }}
 
 The `MultipartID` metadata MAY be used with the
-[`acq-<label>`](../99-appendices/09-entities.md#acq) entity, for example:
+[`acq-<label>`](../appendices/entities.md#acq) entity, for example:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -794,7 +794,8 @@ The `*_aslcontext.tsv` table consists of a single column of labels identifying t
 Volume types are defined in the following table, based on DICOM Tag 0018, 9257 `ASL Context`.
 Note that the volume_types `control` and  `label` within BIDS only serve
 to specify the magnetization state of the blood and thus the ASL subtraction order.
-See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#which-image-is-control-and-which-is-label) for more information on `control` and  `label`.
+See the [ASL Appendix](../appendices/arterial-spin-labeling.md#which-image-is-control-and-which-is-label)
+for more information on `control` and  `label`.
 
 | **volume_type** | **Definition**                                                                                                                                                                         |
 | --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
@@ -812,7 +813,7 @@ If the `deltam` is not available,
 When `cbf` is stored within the `*_asl.nii[.gz]`,
 its units need to be specified in the `*_asl.json` as well.
 Note that the raw images, including the `m0scan`, may also be used for quality control.
-See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#_aslcontexttsv-three-possible-cases) for examples of the three possible cases, in order of decreasing preference.
+See the [ASL Appendix](../appendices/arterial-spin-labeling.md#_aslcontexttsv-three-possible-cases) for examples of the three possible cases, in order of decreasing preference.
 
 ### Scaling
 
@@ -836,7 +837,7 @@ Additionally, some common metadata fields are REQUIRED for the `*_asl.json`:
 `MagneticFieldStrength`, `MRAcquisitionType`, `EchoTime`,
 `SliceTiming` in case `MRAcquisitionType` is defined as 2D,
 `RepetitionTimePreparation`, and `FlipAngle` in case `LookLocker` is `true`.
-See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#summary-image-of-the-most-common-asl-sequences) for more information on the most common ASL sequences.
+See the [ASL Appendix](../appendices/arterial-spin-labeling.md#summary-image-of-the-most-common-asl-sequences) for more information on the most common ASL sequences.
 
 #### Common metadata fields applicable to both (P)CASL and PASL
 
@@ -852,7 +853,7 @@ A guide for using macros can be found at
 
 #### (P)CASL-specific metadata fields
 
-These fields can only be used when `ArterialSpinLabelingType` is `"CASL"` or `"PCASL"`. See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#pcasl-sequence) for more information on the (P)CASL sequence and the Labeling Pulse fields.
+These fields can only be used when `ArterialSpinLabelingType` is `"CASL"` or `"PCASL"`. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#pcasl-sequence) for more information on the (P)CASL sequence and the Labeling Pulse fields.
 
 <!-- This block generates a metadata table.
 These tables are defined in
@@ -870,7 +871,7 @@ A guide for using macros can be found at
 
 #### PASL-specific metadata fields
 
-These fields can only be used when `ArterialSpinLabelingType` is `PASL`. See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#pasl-sequence) for more information on the PASL sequence and the BolusCutOff fields.
+These fields can only be used when `ArterialSpinLabelingType` is `PASL`. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#pasl-sequence) for more information on the PASL sequence and the BolusCutOff fields.
 
 <!-- This block generates a metadata table.
 These tables are defined in
@@ -897,7 +898,7 @@ A guide for using macros can be found at
 {{ MACROS___make_sidecar_table("asl.MRIASLM0Scan") }}
 
 The following table recapitulates the ASL field dependencies. If Source field (column 1) contains the Value specified in column 2, then the Requirements in column 4 are
-imposed on the Dependent fields in column 3. See [Appendix XII](../99-appendices/12-arterial-spin-labeling.md#flowchart-based-on-dependency-table) for this information in the
+imposed on the Dependent fields in column 3. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#flowchart-based-on-dependency-table) for this information in the
 form of flowcharts.
 
 | **Source field**         | **Value**    | **Dependent field**  | **Requirements**                                 |
@@ -1146,7 +1147,7 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["epi"]) }}
 
-The [`dir-<label>`](../99-appendices/09-entities.md#dir) entity is REQUIRED
+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
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 633c85e11b..c6ba494dd4 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -58,7 +58,7 @@ limit.
 For example Neuromag/Elekta/Megin, which can produce several files
 for a single recording.
 Both `some_file.fif` and `some_file-1.fif` would belong to a single recording.
-In BIDS, the [`split`](../99-appendices/09-entities.md#split) entity is RECOMMENDED to deal
+In BIDS, the [`split`](../appendices/entities.md#split) entity is RECOMMENDED to deal
 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
@@ -70,11 +70,11 @@ which saves the MEG sensor coil positions in a separate file with two possible f
 For these files, the `markers` suffix MUST be used.
 For example: `sub-01_task-nback_markers.sqd`
 
-Please refer to [Appendix VI](../99-appendices/06-meg-file-formats.md)
+Please refer to the [MEG File Formats Appendix](../appendices/meg-file-formats.md)
 for general information on how to deal with such manufacturer specifics and to see more examples.
 
-The [`proc-<label>`](../99-appendices/09-entities.md#proc) entity is analogous to the
-[`rec-<label>`](../99-appendices/09-entities.md#rec) entity for MRI,
+The [`proc-<label>`](../appendices/entities.md#proc) entity is analogous to the
+[`rec-<label>`](../appendices/entities.md#rec) entity for MRI,
 and denotes a variant of a file that was a result of particular processing performed on the device.
 This is useful for files produced in particular by Elekta's MaxFilter
 (for example, sss, tsss, trans, quat, mc),
@@ -92,7 +92,8 @@ If however EEG is recorded simultaneously **with the same MEG system**,
 it MAY be stored under the `/meg` data type.
 In that case, it SHOULD have the same sampling frequency as MEG (see `SamplingFrequency` field below).
 Furthermore, the EEG sensor coordinates SHOULD be specified using MEG-specific coordinate
-systems (see [coordinates section](#coordinate-system-json-_coordsystemjson) below and [Appendix VIII](../99-appendices/08-coordinate-systems.md)).
+systems (see [coordinates section](#coordinate-system-json-_coordsystemjson) below and
+the [Coordinate Systems Appendix](../appendices/coordinate-systems.md)).
 
 ### Sidecar JSON (`*_meg.json`)
 
@@ -441,7 +442,7 @@ taped to the skin. Please note that the photos may need to be cropped or blurred
 to conceal identifying features prior to sharing, depending on the terms of the
 consent given by the participant.
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to indicate acquisition of different photos of
+The [`acq-<label>`](../appendices/entities.md#acq) entity can be used to indicate acquisition of different photos of
 the same face (or other body part in different angles to show, for example, the
 location of the nasion (NAS) as opposed to the right periauricular point (RPA)).
 
@@ -465,10 +466,10 @@ This file is RECOMMENDED.
 
 The 3-D locations of points that describe the head shape and/or EEG
 electrode locations can be digitized and stored in separate files. The
-[`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used when more than one type of digitization in done for
+[`acq-<label>`](../appendices/entities.md#acq) entity can be used when more than one type of digitization in done for
 a session, for example when the head points are in a separate file from the EEG
 locations. These files are stored in the specific format of the 3-D digitizer’s
-manufacturer (see [Appendix VI](../99-appendices/06-meg-file-formats.md)).
+manufacturer (see the [MEG File Formats Appendix](../appendices/meg-file-formats.md)).
 
 Example:
 
@@ -495,20 +496,20 @@ has to be updated, then for MEG it could be considered to be a new session.
 
 Empty-room MEG recordings capture the environmental and recording system's noise.
 
-It is RECOMMENDED to explicitly specify which empty-room recording should be used with which experimental run(s) or session(s). This can be done via the [`AssociatedEmptyRoom`](../99-appendices/14-glossary.md#associatedemptyroom-metadata) field in the `*_meg.json` sidecar files.
+It is RECOMMENDED to explicitly specify which empty-room recording should be used with which experimental run(s) or session(s). This can be done via the [`AssociatedEmptyRoom`](../glossary.md#associatedemptyroom-metadata) field in the `*_meg.json` sidecar files.
 
 Empty-room recordings may be collected once per day, where a single empty-room recording may be shared between multiple subjects and/or sessions (see example 1).
 Empty-room recordings can also be collected for each individual experimental session (see example 2).
 
 In the case of empty-room recordings being associated with multiple subjects and/or sessions, it is RECOMMENDED to store the empty-room recording inside a subject directory named `sub-emptyroom`.
-If a [`session-<label>`](../99-appendices/09-entities.md#ses) entity is present, its label SHOULD be the date of the empty-room recording in the format `YYYYMMDD`, that is `ses-YYYYMMDD`.
+If a [`session-<label>`](../appendices/entities.md#ses) entity is present, its label SHOULD be the date of the empty-room recording in the format `YYYYMMDD`, that is `ses-YYYYMMDD`.
 The `scans.tsv` file containing the date and time of the acquisition SHOULD also be included.
 The rationale is that this naming scheme will allow users to easily retrieve the empty-room recording that best matches a particular experimental session, based on date and time of the recording.
 It should be possible to query empty-room recordings just like usual subject recordings, hence all metadata sidecar files (such as the `channels.tsv`) file SHOULD be present as well.
 
 In the case of empty-room recordings being collected for the individual experimental session, it is recommended to store the empty-room recording along with that subject and session.
 
-In either case, the label for the [`task-<label>`](../99-appendices/09-entities.md#task) entity in the empty-room recording SHOULD be set to `noise`.
+In either case, the label for the [`task-<label>`](../appendices/entities.md#task) entity in the empty-room recording SHOULD be set to `noise`.
 
 Example 1:
 
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
index 39043f7e96..fe64f59628 100644
--- a/src/04-modality-specific-files/03-electroencephalography.md
+++ b/src/04-modality-specific-files/03-electroencephalography.md
@@ -348,7 +348,7 @@ Cz     0.0000   0.0714   0.0699   cup      Ag/AgCl
 REF    -0.0742  -0.0200  -0.0100  cup      Ag/AgCl
 ```
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to
+The [`acq-<label>`](../appendices/entities.md#acq) entity can be used to
 indicate acquisition of the same data. For
 example, this could be the recording of electrode positions with a different
 electrode position recording device, or repeated digitization before and after
@@ -488,7 +488,7 @@ Please note that the photos may need to be cropped or blurred to conceal
 identifying features prior to sharing, depending on the terms of the consent
 given by the participant.
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity can be used to
+The [`acq-<label>`](../appendices/entities.md#acq) entity can be used to
 indicate acquisition of different photos of
 the same face (or other body part in different angles to show, for example, the
 location of the nasion (NAS) as opposed to the right periauricular point (RPA).
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
index fc0fd76006..1ae672a974 100644
--- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md
+++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
@@ -320,12 +320,12 @@ that coordinates are expected in cartesian coordinates according to the
 `*_coordsystem.json`. If an `*_electrodes.tsv` file is specified, a
 `*_coordsystem.json` file MUST be specified as well.
 
-The optional [`space-<label>`](../99-appendices/09-entities.md#space) entity (`*[_space-<label>]_electrodes.tsv`) can be used to
+The optional [`space-<label>`](../appendices/entities.md#space) entity (`*[_space-<label>]_electrodes.tsv`) can be used to
 indicate the way in which electrode positions are interpreted.
 The space `<label>` MUST be taken from one of the modality specific lists in
-[Appendix VIII](../99-appendices/08-coordinate-systems.md).
+the [Coordinate Systems Appendix](../appendices/coordinate-systems.md).
 For example for iEEG data, the restricted keywords listed under
-[iEEG Specific Coordinate Systems](../99-appendices/08-coordinate-systems.md#ieeg-specific-coordinate-systems)
+[iEEG Specific Coordinate Systems](../appendices/coordinate-systems.md#ieeg-specific-coordinate-systems)
 are acceptable for `<label>`.
 
 For examples:
@@ -337,7 +337,7 @@ For examples:
     space)
 
 When referring to the `*_electrodes.tsv` file in a certain _space_ as defined
-above, the [`space-<label>`](../99-appendices/09-entities.md#space) of the accompanying `*_coordsystem.json` MUST
+above, the [`space-<label>`](../appendices/entities.md#space) of the accompanying `*_coordsystem.json` MUST
 correspond.
 
 For example:
@@ -463,7 +463,7 @@ A guide for using macros can be found at
 
 It is preferred that electrodes are localized in a 3D coordinate system (with
 respect to a pre- and/or post-operative anatomical MRI or CT scans or in a
-standard space as specified in BIDS [Appendix VIII](../99-appendices/08-coordinate-systems.md)
+standard space as specified in the BIDS [Coordinate Systems Appendix](../appendices/coordinate-systems.md)
 about preferred names of coordinate systems, such as ACPC).
 
 ### Allowed 2D coordinate systems
@@ -480,10 +480,10 @@ with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the
 ### Multiple coordinate systems
 
 If electrode positions are known in multiple coordinate systems (for example, MRI, CT
-and MNI), these spaces can be distinguished by the optional [`space-<label>`](../99-appendices/09-entities.md#space)
+and MNI), these spaces can be distinguished by the optional [`space-<label>`](../appendices/entities.md#space)
 field, see the [`*_electrodes.tsv`-section](#electrode-description-_electrodestsv)
 for more information.
-Note that the [`space-<label>`](../99-appendices/09-entities.md#space) fields must correspond
+Note that the [`space-<label>`](../appendices/entities.md#space) fields must correspond
 between `*_electrodes.tsv` and `*_coordsystem.json` if they refer to the same
 data.
 
@@ -518,7 +518,7 @@ during surgery, or screenshots of a brain rendering with electrode positions.
 The photos may need to be cropped and/or blurred to conceal identifying features
 or entirely omitted prior to sharing, depending on obtained consent.
 
-If there are photos of the electrodes, the [`acq-<label>`](../99-appendices/09-entities.md#acq) entity should be specified
+If there are photos of the electrodes, the [`acq-<label>`](../appendices/entities.md#acq) entity should be specified
 with:
 
 -   `*_photo.jpg` in case of an operative photo
@@ -530,7 +530,7 @@ with:
 
 -   `*_acq-render#_photo.jpg` in case of a rendering
 
-The [`ses-<label>`](../99-appendices/09-entities.md#ses) entity may be used to specify when the photo was taken.
+The [`ses-<label>`](../appendices/entities.md#ses) entity may be used to specify when the photo was taken.
 
 Example of the operative photo of ECoG electrodes (here is an annotated example in
 which electrodes and vasculature are marked, taken from Hermes et al.,
diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md
index 9547c10de4..8b0fcff794 100644
--- a/src/04-modality-specific-files/05-task-events.md
+++ b/src/04-modality-specific-files/05-task-events.md
@@ -139,7 +139,7 @@ Note: Events can also be documented in machine-actionable form
 using HED (Hierarchical Event Descriptor) tags.
 This type of documentation is particularly useful for datasets likely to be used
 in event-related analyses.
-See [Hierarchical Event Descriptors](../99-appendices/03-hed.md)
+See [Hierarchical Event Descriptors](../appendices/hed.md)
 for additional information and examples.
 
 ## Stimuli
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
index 53176a36fe..a715de61d4 100644
--- a/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
+++ b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
@@ -39,7 +39,7 @@ For example for the file `sub-control01_task-nback_run-1_bold.nii.gz`,
 Note that when supplying a `*_<physio|stim>.tsv.gz` file, an accompanying
 `*_<physio|stim>.json` MUST be supplied as well.
 
-The [`recording-<label>`](../99-appendices/09-entities.md#recording)
+The [`recording-<label>`](../appendices/entities.md#recording)
 entity MAY be used to distinguish between several recording files.
 For example `sub-01_task-bart_recording-eyetracking_physio.tsv.gz` to contain
 the eyetracking data in a certain sampling frequency, and
@@ -166,7 +166,7 @@ as deemed appropriate by the researcher.
 
 Recordings with different sampling frequencies or starting times should be
 stored in separate files
-(and the [`recording-<label>`](../99-appendices/09-entities.md#recording)
+(and the [`recording-<label>`](../appendices/entities.md#recording)
 entity MAY be used to distinguish these files).
 
 If the same continuous recording has been used for all subjects (for example in
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
index f5c5b515e4..b6e57316b8 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -23,10 +23,10 @@ rather than `_events.tsv`.
 
 Each task has a unique label that MUST only consist of letters and/or numbers
 (other characters, including spaces and underscores, are not allowed) with the
-[`task-<label>`](../99-appendices/09-entities.md#task) entity.
+[`task-<label>`](../appendices/entities.md#task) entity.
 Those labels MUST be consistent across subjects and sessions.
 
-The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label to
+The OPTIONAL [`acq-<label>`](../appendices/entities.md#acq) entity corresponds to a custom label to
 distinguish different conditions present during multiple runs of the same task.
 For example, if a study includes runs of an n-back task, with deep brain
 stimulation turned on or off, the data files may be labelled
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 2a687c4f74..8b3e1d276b 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -77,13 +77,13 @@ PET imaging data SHOULD be stored in 4D (or 3D, if only one volume was acquired)
 NIfTI files with the `_pet` suffix.
 Volumes MUST be stored in chronological order (the order they were acquired in).
 
-The OPTIONAL [`task-<label>`](../99-appendices/09-entities.md#task) is used to
+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
 (please note that this file is not necessary for resting scans).
 
-The [`trc-<label>`](../99-appendices/09-entities.md#trc) entity is used to
+The [`trc-<label>`](../appendices/entities.md#trc) entity is used to
 indicate the tracer used.
 This entity is OPTIONAL if only one tracer is used in the study,
 but REQUIRED to distinguish between tracers if multiple are used.
@@ -94,11 +94,11 @@ Other labels are permitted, as long as they are consistent across subjects and s
 and consist only of the legal label characters.
 
 If more than one run of the same task and acquisition (tracer) are acquired during
-the same session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
+the same session, the [`run-<index>`](../appendices/entities.md#run) entity MUST be used:
 `_run-1`, `_run-2`, `_run-3`, and so on.
 If only one run was acquired the `run-<index>` can be omitted.
 
-The OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec) entity
+The OPTIONAL [`rec-<label>`](../appendices/entities.md#rec) entity
 is used to indicate the reconstruction method used for the image,
 with four reserved values:
 
@@ -120,11 +120,11 @@ it is essential to specify whether MR images have been corrected for gradient no
 using the `NonLinearGradientCorrection` metadata field
 (see [Sequence Specifics](./01-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](../99-appendices/13-cross-modality-correspondence.md#pet-mri-correspondence)).
+(see also [PET-MRI correspondence](../appendices/cross-modality-correspondence.md#pet-mri-correspondence)).
 In the case of studies using combined PET/fMRI,
 subject-specific tasks may be carried out during the acquisition within the same session.
 If the same task is recorded with both modalities,
-the same [`task-<label>`](../99-appendices/09-entities.md#task) entity SHOULD be used.
+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).
 
@@ -204,7 +204,7 @@ All reconstruction-specific parameters that are not specified, but one wants to
 
 #### Task
 
-If the OPTIONAL [`task-<label>`](../99-appendices/09-entities.md#task) is used,
+If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,
 the following metadata SHOULD be used.
 
 <!-- This block generates a metadata table.
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index a6cbf54a6f..464096d726 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -95,12 +95,12 @@ and a guide for using macros can be found at
 
 ### Filename entities
 
-In the context of Microscopy, a session ([`ses-<label>`](../99-appendices/09-entities.md#ses))
+In the context of Microscopy, a session ([`ses-<label>`](../appendices/entities.md#ses))
 can refer to all the acquisitions between the start and the end of an imaging experiment
 for ex vivo imaging, or a subject lab visit for biopsy procedure and/or in vivo imaging.
 Consistent with other data types in BIDS, the session entity is optional.
 
-The [`sample-<label>`](../99-appendices/09-entities.md#sample) entity is REQUIRED for
+The [`sample-<label>`](../appendices/entities.md#sample) entity is REQUIRED for
 Microscopy data and is used to distinguish between different samples from the same subject.
 The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
 
@@ -128,7 +128,7 @@ 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).
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity corresponds to a custom label that
+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.
 For example, two images of the same sample acquired by bright-field microscopy (BF) in PNG format at
 different magnification of 40x and 60x.
@@ -136,7 +136,7 @@ In such case two files could have the following names: `sub-01_sample-01_acq-40x
 `sub-01_sample-01_acq-60x_BF.png`, however the user is free to choose any other label as long as
 they are consistent across subjects and sessions.
 
-The [`stain-<label>`](../99-appendices/09-entities.md#stain) entity MAY be used to distinguish
+The [`stain-<label>`](../appendices/entities.md#stain) entity MAY be used to distinguish
 image files from the same sample using different stains or antibodies for contrast enhancement.
 
 For example: One brain slice (`sample-01`) extracted from subject `sub-01` with three
@@ -173,11 +173,11 @@ Description of antibodies SHOULD also be indicated in `"SamplePrimaryAntibodies"
 and/or `"SampleSecondaryAntobodies"` as appropriate.
 
 If more than one run of the same sample, acquisition and stain are acquired during the same
-session, the [`run-<index>`](../99-appendices/09-entities.md#run) entity MUST be used:
+session, the [`run-<index>`](../appendices/entities.md#run) entity MUST be used:
 `_run-1`, `_run-2`, `_run-3`, and so on.
 If only one run was acquired the `run-<index>` can be omitted.
 
-The [`chunk-<index>`](../99-appendices/09-entities.md#chunk) entity is used when multiples
+The [`chunk-<index>`](../appendices/entities.md#chunk) entity is used when multiples
 regions (2D images or 3D volumes files) of the same physical sample are imaged with different
 fields of view, regardless if they overlap or not.
 
@@ -234,7 +234,7 @@ In microscopy, many pyramidal file formats store multiple resolutions for the sa
 In the case where a multiple resolutions file format is converted to single resolution file format,
 only the higher resolution file is present in the raw data.
 Lower resolutions files MUST be placed under the `derivatives` directory and use the
-[`res-<label>`](../99-appendices/09-entities.md#res) entity.
+[`res-<label>`](../appendices/entities.md#res) entity.
 
 For example:
 
@@ -442,7 +442,7 @@ and a guide for using macros can be found at
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.
 
-The [`acq-<label>`](../99-appendices/09-entities.md#acq) entity MAY be used to indicate
+The [`acq-<label>`](../appendices/entities.md#acq) entity MAY be used to indicate
 acquisition of different photos of the same sample.
 
 For example:
diff --git a/src/05-derivatives/01-introduction.md b/src/05-derivatives/01-introduction.md
index f2dcdf38ab..195422f9e0 100644
--- a/src/05-derivatives/01-introduction.md
+++ b/src/05-derivatives/01-introduction.md
@@ -57,7 +57,7 @@ in [Derived dataset and pipeline description][derived-dataset-description].
     files.
 
 -   When necessary to distinguish two files that do not otherwise have a
-    distinguishing entity, the [`_desc-<label>`](../99-appendices/09-entities.md#desc)
+    distinguishing entity, the [`_desc-<label>`](../appendices/entities.md#desc)
     entity SHOULD be used.
     This includes the cases of needing to distinguish both differing inputs and
     differing outputs (for example, `_desc-T1w` and `_desc-T2w` to distinguish
@@ -68,7 +68,7 @@ in [Derived dataset and pipeline description][derived-dataset-description].
 -   When naming files that are not yet standardized, it is RECOMMENDED to use
     names consistent with BIDS conventions where those conventions apply.
     For example, if a summary statistic is derived from a given task, the file
-    name SHOULD contain [`_task-<label>`](../99-appendices/09-entities.md#task).
+    name SHOULD contain [`_task-<label>`](../appendices/entities.md#task).
 
 <!-- Link Definitions -->
 
diff --git a/src/05-derivatives/02-common-data-types.md b/src/05-derivatives/02-common-data-types.md
index 2d9616a1dc..ac672f64e0 100644
--- a/src/05-derivatives/02-common-data-types.md
+++ b/src/05-derivatives/02-common-data-types.md
@@ -24,7 +24,7 @@ A guide for using macros can be found at
 
 Preprocessed `bold` NIfTI file in the original coordinate space of the original run.
 The location of the file in the original datasets is encoded in the `Sources` metadata,
-and [`_desc-<label>`](../99-appendices/09-entities.md#desc)
+and [`_desc-<label>`](../appendices/entities.md#desc)
 is used to prevent clashing with the original filename.
 
 <!-- This block generates a file tree.
@@ -85,12 +85,12 @@ and the raw original file.
 Derivatives are often aligned to a common spatial reference to allow for the
 comparison of acquired data across runs, sessions, subjects or datasets.
 A file may indicate the spatial reference to which it has been aligned using the
-[`space` entity](../99-appendices/09-entities.md#space) and/or the `SpatialReference` metadata.
+[`space` entity](../appendices/entities.md#space) and/or the `SpatialReference` metadata.
 
-The [`space` entity](../99-appendices/09-entities.md#space) may take any value in
+The [`space` entity](../appendices/entities.md#space) may take any value in
 [Image-Based Coordinate Systems][coordsys].
 
-If the [`space` entity](../99-appendices/09-entities.md#space) is omitted,
+If the [`space` entity](../appendices/entities.md#space) is omitted,
 or the space is not in the [Standard template identifiers][templates] table,
 then the `SpatialReference` metadata is REQUIRED.
 
@@ -198,11 +198,11 @@ Examples of preprocessing:
 -   Time-domain filtered EEG data
 -   MaxFilter (for example, SSS) cleaned MEG data
 
-The [`space` entity](../99-appendices/09-entities.md#space)
+The [`space` entity](../appendices/entities.md#space)
 is recommended to distinguish files with different underlying
 coordinate systems or registered to different reference maps.
 See [Spatial references](#spatial-references) for details.
-The [`desc` entity](../99-appendices/09-entities.md#desc) ("description")
+The [`desc` entity](../appendices/entities.md#desc) ("description")
 is a general purpose field with freeform values,
 which SHOULD be used to distinguish between multiple different versions of
 processing for the same input data.
@@ -256,9 +256,9 @@ static volume, a `RepetitionTime` property would no longer be relevant).
 
 <!-- Link Definitions -->
 
-[coordsys]: ../99-appendices/08-coordinate-systems.md#image-based-coordinate-systems
+[coordsys]: ../appendices/coordinate-systems.md#image-based-coordinate-systems
 
-[templates]: ../99-appendices/08-coordinate-systems.md#standard-template-identifiers
+[templates]: ../appendices/coordinate-systems.md#standard-template-identifiers
 
 [object]: https://www.json.org/json-en.html
 
diff --git a/src/05-derivatives/03-imaging.md b/src/05-derivatives/03-imaging.md
index bc14afc45d..3a93d112f4 100644
--- a/src/05-derivatives/03-imaging.md
+++ b/src/05-derivatives/03-imaging.md
@@ -22,13 +22,13 @@ sufficiently similar in practice to treat them equivalently.
 
 When two or more instances of a given derivative are provided with resolution
 or surface sampling density being the only difference between them, then the
-[`res`](../99-appendices/09-entities.md#res) (for *resolution* of regularly sampled N-D data) and/or
-[`den`](../99-appendices/09-entities.md#den) (for *density* of non-parametric surfaces)
+[`res`](../appendices/entities.md#res) (for *resolution* of regularly sampled N-D data) and/or
+[`den`](../appendices/entities.md#den) (for *density* of non-parametric surfaces)
 entities SHOULD be used to avoid name conflicts.
 Note that only files combining both regularly sampled (for example, gridded)
 and surface sampled data (and their downstream derivatives) are allowed
-to present both [`res`](../99-appendices/09-entities.md#res) and
-[`den`](../99-appendices/09-entities.md#den) entities simultaneously.
+to present both [`res`](../appendices/entities.md#res) and
+[`den`](../appendices/entities.md#den) entities simultaneously.
 
 Examples:
 
@@ -101,8 +101,8 @@ And one corresponding to `res-hi`
 ```
 
 Example of CIFTI-2 files (a format that combines regularly sampled data
-and non-parametric surfaces) having both [`res`](../99-appendices/09-entities.md#res)
-and [`den`](../99-appendices/09-entities.md#den) entities:
+and non-parametric surfaces) having both [`res`](../appendices/entities.md#res)
+and [`den`](../appendices/entities.md#den) entities:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -151,9 +151,9 @@ Template:
             <source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>][_desc-<label>]_mask.nii.gz
 ```
 
-A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../99-appendices/09-entities.md#space).
+A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
 If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
-If the mask is an ROI mask derived from an atlas, then the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD
+If the mask is an ROI mask derived from an atlas, then the [`label` entity](../appendices/entities.md#label)) SHOULD
 be used to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
 and the `Atlas` metadata SHOULD be defined.
@@ -230,7 +230,7 @@ Segmentations may be defined in a volume (labeled voxels), a surface (labeled
 vertices) or a combined volume/surface space.
 
 If the segmentation can be derived from different atlases,
-the [`atlas` entity](../99-appendices/09-entities.md#atlas) MAY be used to
+the [`atlas` entity](../appendices/entities.md#atlas) MAY be used to
 distinguish the different segmentations.
 If so, the `Atlas` metadata SHOULD also be defined.
 
@@ -293,10 +293,10 @@ A guide for using macros can be found at
 A segmentation can be used to generate a binary mask that functions as a
 discrete "label" for a single structure.
 In this case, the mask suffix MUST be used,
-the [`label` entity](../99-appendices/09-entities.md#label)) SHOULD be used
+the [`label` entity](../appendices/entities.md#label)) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
-the [`atlas` entity](../99-appendices/09-entities.md#atlas) and the
+the [`atlas` entity](../appendices/entities.md#atlas) and the
 `Atlas` metadata SHOULD be defined.
 
 For example:
@@ -324,7 +324,7 @@ Probabilistic segmentations of brain tissue represent a single anatomical
 structure with values ranging from 0 to 1 in individual 3D volumes or across
 multiple frames.
 If a single structure is included,
-the [`label` entity](../99-appendices/09-entities.md#label) SHOULD be used to specify
+the [`label` entity](../appendices/entities.md#label) SHOULD be used to specify
 the structure.
 
 Template:
@@ -356,7 +356,7 @@ A guide for using macros can be found at
 ) }}
 
 See [Common image-derived labels](#common-image-derived-labels)
-for reserved values for the [`label`](../99-appendices/09-entities.md#label) entity.
+for reserved values for the [`label`](../appendices/entities.md#label) entity.
 
 A 4D probabilistic segmentation, in which each frame corresponds to a different
 tissue class, must provide a label mapping in its JSON sidecar. For example:
@@ -410,7 +410,7 @@ Template:
             <source_entities>[_hemi-{L|R}][_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
 ```
 
-The [`hemi-<label>`](../99-appendices/09-entities.md#hemi) entity is REQUIRED for GIFTI files storing information about
+The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about
 a structure that is restricted to a hemibrain.
 For example:
 
diff --git a/src/99-appendices/12-arterial-spin-labeling.md b/src/appendices/arterial-spin-labeling.md
similarity index 99%
rename from src/99-appendices/12-arterial-spin-labeling.md
rename to src/appendices/arterial-spin-labeling.md
index cd834bfbbf..35b7723806 100644
--- a/src/99-appendices/12-arterial-spin-labeling.md
+++ b/src/appendices/arterial-spin-labeling.md
@@ -1,4 +1,4 @@
-# Appendix XI: Arterial Spin Labeling
+# Arterial Spin Labeling
 
 These sections provide additional clarification for some specific topics within the BIDS specification for Arterial Spin Labeling.
 
diff --git a/src/99-appendices/01-contributors.md b/src/appendices/contributors.md
similarity index 99%
rename from src/99-appendices/01-contributors.md
rename to src/appendices/contributors.md
index 0e22113de1..03698ed5f9 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/appendices/contributors.md
@@ -1,4 +1,4 @@
-# Appendix I: Contributors
+# Contributors
 
 Legend (source:
 <https://allcontributors.org/docs/en/emoji-key>)
diff --git a/src/99-appendices/08-coordinate-systems.md b/src/appendices/coordinate-systems.md
similarity index 99%
rename from src/99-appendices/08-coordinate-systems.md
rename to src/appendices/coordinate-systems.md
index b8aeaa179a..91273835c7 100644
--- a/src/99-appendices/08-coordinate-systems.md
+++ b/src/appendices/coordinate-systems.md
@@ -1,4 +1,4 @@
-# Appendix VIII: Coordinate systems
+# Coordinate systems
 
 ## Introduction
 
diff --git a/src/99-appendices/13-cross-modality-correspondence.md b/src/appendices/cross-modality-correspondence.md
similarity index 94%
rename from src/99-appendices/13-cross-modality-correspondence.md
rename to src/appendices/cross-modality-correspondence.md
index a153b40ef9..f77598d147 100644
--- a/src/99-appendices/13-cross-modality-correspondence.md
+++ b/src/appendices/cross-modality-correspondence.md
@@ -1,4 +1,4 @@
-# Appendix XIII: Cross modality correspondence
+# Cross modality correspondence
 
 ## PET-MRI correspondence
 
diff --git a/src/99-appendices/09-entities.md b/src/appendices/entities.md
similarity index 93%
rename from src/99-appendices/09-entities.md
rename to src/appendices/entities.md
index 03daf3ef33..06101ce0d0 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/appendices/entities.md
@@ -1,4 +1,4 @@
-# Appendix IX: Entities
+# Entities
 
 This section compiles the entities (key-value pairs within file names) described throughout this
 specification, and describes each.
@@ -7,7 +7,7 @@ A general introduction to entities is given in the section on
 [filename structure](../02-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](04-entity-table.md).
+be specified for a given file type, is specified in the [Entity Table](entity-table.md).
 
 <!--
   This section is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
diff --git a/src/99-appendices/04-entity-table.md b/src/appendices/entity-table.md
similarity index 94%
rename from src/99-appendices/04-entity-table.md
rename to src/appendices/entity-table.md
index 8cd135b0b8..f07c69982b 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/appendices/entity-table.md
@@ -1,4 +1,4 @@
-# Appendix IV: Entity table
+# Entity table
 
 This section compiles the entities (key-value pairs within file names) described throughout this
 specification, and establishes a common order within a filename.
@@ -11,7 +11,7 @@ Entity formats indicate whether the value is alphanumeric
 
 A general introduction to entities is given in the section on
 [filename structure](../02-common-principles.md#file-name-structure),
-while entity definitions are in [Appendix IX](09-entities.md).
+while entity definitions are in the [Entities Appendix](entities.md).
 
 <!--
   This file is autogenerated based on the src/schema.  DO NOT EDIT DIRECTLY.
diff --git a/src/99-appendices/10-file-collections.md b/src/appendices/file-collections.md
similarity index 71%
rename from src/99-appendices/10-file-collections.md
rename to src/appendices/file-collections.md
index ce95bd8146..38102b5a98 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/appendices/file-collections.md
@@ -1,4 +1,4 @@
-# Appendix X: File collections
+# 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.
 
@@ -12,11 +12,11 @@ Please keep the following list of linking entities up-to-date with the file coll
 included in this appendix:
 
 -   Magnetic Resonance Imaging
-    -   [`echo`](./09-entities.md#echo)
-    -   [`flip`](./09-entities.md#flip)
-    -   [`inv`](./09-entities.md#inv)
-    -   [`mt`](./09-entities.md#mt)
-    -   [`part`](./09-entities.md#part)
+    -   [`echo`](./entities.md#echo)
+    -   [`flip`](./entities.md#flip)
+    -   [`inv`](./entities.md#inv)
+    -   [`mt`](./entities.md#mt)
+    -   [`part`](./entities.md#part)
 
 ## Magnetic Resonance Imaging
 
@@ -76,12 +76,12 @@ and a guide for using macros can be found at
     ])
 }}
 
-| **Suffix** | **Meta-data relevant entity**                                | **Application**                    | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-|------------|--------------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| TB1DAM     | flip                                                         | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                        |
-| TB1EPI     | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                       |
-| TB1AFI     | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                               |
-| TB1TFL     | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
-| TB1RFM     | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                |
-| TB1SRGE    | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
-| RB1COR     | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                 |
+| **Suffix** | **Meta-data relevant entity**                          | **Application**                    | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                         |
+|------------|--------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| TB1DAM     | flip                                                   | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                        |
+| TB1EPI     | flip, echo                                             | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                       |
+| TB1AFI     | Please see the [qMRI appendix](../appendices/qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                               |
+| TB1TFL     | Please see the [qMRI appendix](../appendices/qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
+| TB1RFM     | Please see the [qMRI appendix](../appendices/qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                |
+| TB1SRGE    | `flip`, `inv`                                          | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
+| RB1COR     | Please see the [qMRI appendix](../appendices/qmri.md). | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                 |
diff --git a/src/99-appendices/03-hed.md b/src/appendices/hed.md
similarity index 99%
rename from src/99-appendices/03-hed.md
rename to src/appendices/hed.md
index e6dc12c959..77677a00ab 100644
--- a/src/99-appendices/03-hed.md
+++ b/src/appendices/hed.md
@@ -1,4 +1,4 @@
-# Appendix III: Hierarchical Event Descriptors
+# Hierarchical Event Descriptors
 
 Hierarchical Event Descriptors (HED) are a controlled vocabulary of terms describing
 events in a machine-actionable form so that algorithms can use the information without
diff --git a/src/99-appendices/02-licenses.md b/src/appendices/licenses.md
similarity index 98%
rename from src/99-appendices/02-licenses.md
rename to src/appendices/licenses.md
index a735db74a2..90cb6aa73f 100644
--- a/src/99-appendices/02-licenses.md
+++ b/src/appendices/licenses.md
@@ -1,4 +1,4 @@
-# Appendix II: Licenses
+# Licenses
 
 This section lists a number of common licenses for datasets and defines
 suggested abbreviations for use in the dataset metadata specifications.
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/appendices/meg-file-formats.md
similarity index 92%
rename from src/99-appendices/06-meg-file-formats.md
rename to src/appendices/meg-file-formats.md
index 790efffecd..8da4d31edb 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/appendices/meg-file-formats.md
@@ -1,16 +1,16 @@
-# Appendix VI: MEG file formats
+# MEG file formats
 
 Each MEG system brand has specific file organization and data formats.
 RECOMMENDED values for `manufacturer_specific_extensions`:
 
-| **Value**                                           | **Description**                                                                       |
-| --------------------------------------------------- | ------------------------------------------------------------------------------------- |
-| [`ctf`](06-meg-file-formats.md#ctf)                 | CTF (directory with `.ds` extension)                                                  |
-| [`fif`](06-meg-file-formats.md#neuromagelektamegin) | Neuromag / Elekta / MEGIN and BabyMEG (file with extension `.fif`)                    |
-| [`4d`](06-meg-file-formats.md#bti4d-neuroimaging)   | BTi / 4D Neuroimaging (directory containing multiple files without extensions)        |
-| [`kit`](06-meg-file-formats.md#kityokogawaricoh)    | KIT / Yokogawa / Ricoh (file with extension `.sqd`, `.con`, `.raw`, `.ave` or `.mrk`) |
-| [`kdf`](06-meg-file-formats.md#kriss)               | KRISS (file with extension `.kdf`)                                                    |
-| [`itab`](06-meg-file-formats.md#itab)               | Chieti system (file with extension `.raw` and `.mhd`)                                 |
+| **Value**                     | **Description**                                                                       |
+| ----------------------------- | ------------------------------------------------------------------------------------- |
+| [`ctf`](#ctf)                 | CTF (directory with `.ds` extension)                                                  |
+| [`fif`](#neuromagelektamegin) | Neuromag / Elekta / MEGIN and BabyMEG (file with extension `.fif`)                    |
+| [`4d`](#bti4d-neuroimaging)   | BTi / 4D Neuroimaging (directory containing multiple files without extensions)        |
+| [`kit`](#kityokogawaricoh)    | KIT / Yokogawa / Ricoh (file with extension `.sqd`, `.con`, `.raw`, `.ave` or `.mrk`) |
+| [`kdf`](#kriss)               | KRISS (file with extension `.kdf`)                                                    |
+| [`itab`](#itab)               | Chieti system (file with extension `.raw` and `.mhd`)                                 |
 
 Below are specifications for each system brand.
 
@@ -439,6 +439,6 @@ A guide for using macros can be found at
 
 For stand-alone MEG data, the Aalto hybrid device uses the standard `.fif` data
 format and follows the conventions of Elekta/Neuromag as described
-[above](06-meg-file-formats.md#neuromagelektamegin). The `.fif` files may
+[above](#neuromagelektamegin). The `.fif` files may
 contain unreconstructed MRI data. The inclusion of MRI data and information for
 accurate reconstruction will be fully standardized at a later stage.
diff --git a/src/99-appendices/07-meg-systems.md b/src/appendices/meg-systems.md
similarity index 85%
rename from src/99-appendices/07-meg-systems.md
rename to src/appendices/meg-systems.md
index 4cd22c97e6..ef5bd613d1 100644
--- a/src/99-appendices/07-meg-systems.md
+++ b/src/appendices/meg-systems.md
@@ -1,14 +1,14 @@
-# Appendix VII: MEG systems
+# MEG systems
 
 Preferred names of MEG systems comprise restricted keywords for Manufacturer field in the `*_meg.json` file:
 
--   [`CTF`](06-meg-file-formats.md#ctf)
--   [`Neuromag/Elekta/Megin`](06-meg-file-formats.md#neuromagelektamegin)
--   [`BTi/4D`](06-meg-file-formats.md#bti4d-neuroimaging)
--   [`KIT/Yokogawa/Ricoh`](06-meg-file-formats.md#kityokogawaricoh)
--   [`KRISS`](06-meg-file-formats.md#kriss)
--   [`ITAB`](06-meg-file-formats.md#itab)
--   [`Aalto/MEG-MRI`](06-meg-file-formats.md#aalto-megmri)
+-   [`CTF`](meg-file-formats.md#ctf)
+-   [`Neuromag/Elekta/Megin`](meg-file-formats.md#neuromagelektamegin)
+-   [`BTi/4D`](meg-file-formats.md#bti4d-neuroimaging)
+-   [`KIT/Yokogawa/Ricoh`](meg-file-formats.md#kityokogawaricoh)
+-   [`KRISS`](meg-file-formats.md#kriss)
+-   [`ITAB`](meg-file-formats.md#itab)
+-   [`Aalto/MEG-MRI`](meg-file-formats.md#aalto-megmri)
 -   `Other`
 
 Restricted keywords for ManufacturersModelName field in the `*_meg.json` file:
diff --git a/src/99-appendices/11-qmri.md b/src/appendices/qmri.md
similarity index 98%
rename from src/99-appendices/11-qmri.md
rename to src/appendices/qmri.md
index 3200e67332..dba3c65243 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/appendices/qmri.md
@@ -1,4 +1,4 @@
-# Appendix XI: Quantitative MRI
+# Quantitative MRI
 
 Quantitative MRI (qMRI) is a collection of methods aiming at generating parametric maps
 that can characterize underlying tissue properties.
@@ -88,7 +88,7 @@ A guide for using macros can be found at
    }
 ) }}
 
-Please visit the [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
+Please visit the [file collections appendix](./file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
 
 ### Quantitative maps are derivatives
 
@@ -156,7 +156,7 @@ in the [BIDS examples](https://github.com/bids-standard/bids-examples#qmri-datas
 
 ## Metadata requirements for qMRI data
 
-The table of required entities for qMRI file collections are provided in the [entity table](./04-entity-table.md).
+The table of required entities for qMRI file collections are provided in the [entity table](./entity-table.md).
 However, viability of a qMRI file collection is determined not only by the naming and organization of the input files,
 but also by which metadata fields are provided in accompanying json files.
 
@@ -369,7 +369,7 @@ In this table, (`entity`/`fixed`) denotes whether the OPTIONAL metadata that for
 flavor of qMRI application for the respective suffix varies across files of a file collection
 (which calls for using a linking entity) or fixed. If former is the case, the entity is to be
 added to the files in that file collection. Note that this addition MUST be allowed by the
-priority levels given for that suffix in the [`entity table`](./04-entity-table.md). If latter (`fixed`) is the case,
+priority levels given for that suffix in the [`entity table`](./entity-table.md). If latter (`fixed`) is the case,
 filenames will remain the same; however, the optional metadata (third column) may
 define the flavor of the application (fourth column) along with the conditional value of a
 required metadata field (second column).
@@ -406,7 +406,7 @@ introduce a new suffix:
     (for example, `MP2RAGE`), sequence names are not used as suffixes.
 
 -   File collection suffixes for qMRI applications attain a clear description of the qMRI method that they relate to in the
-    [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging).
+    [file collections appendix](./file-collections.md#magnetic-resonance-imaging).
 
 -   Hyperlinks to example applications and reference method articles are encouraged whenever possible.
 
diff --git a/src/99-appendices/05-units.md b/src/appendices/units.md
similarity index 99%
rename from src/99-appendices/05-units.md
rename to src/appendices/units.md
index 0145398ea4..a375892366 100644
--- a/src/99-appendices/05-units.md
+++ b/src/appendices/units.md
@@ -1,4 +1,4 @@
-# Appendix V: Units
+# Units
 
 As described in the [Units](../02-common-principles.md#units),
 the specification of units SHOULD follow the
diff --git a/src/99-appendices/14-glossary.md b/src/glossary.md
similarity index 90%
rename from src/99-appendices/14-glossary.md
rename to src/glossary.md
index 92bc5540a2..07ac5824c4 100644
--- a/src/99-appendices/14-glossary.md
+++ b/src/glossary.md
@@ -1,4 +1,4 @@
-# Appendix XIV: Glossary of schema objects
+# Glossary of schema objects
 
 This section compiles the object definitions in the schema.
 
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index a3d23738fa..52e7f26fab 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -4,7 +4,7 @@ HED:
   display_name: HED Tag
   description: |
     Hierarchical Event Descriptor (HED) Tag.
-    See [Appendix III](SPEC_ROOT/99-appendices/03-hed.md) for details.
+    See the [HED Appendix](SPEC_ROOT/appendices/hed.md) for details.
   type: string
 abbreviation:
   name: abbreviation
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 4ac5909197..3cd660e856 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -264,14 +264,14 @@ run:
 
     If several data acquisitions (for example, MRI scans or EEG recordings)
     with the same acquisition parameters are acquired in the same session,
-    they MUST be indexed with the [`run-<index>`](../99-appendices/09-entities.md#run) entity:
+    they MUST be indexed with the [`run-<index>`](SPEC_ROOT/appendices/entities.md#run) entity:
     `_run-1`, `_run-2`, `_run-3`, and so on
     (only nonnegative integers are allowed as run indices).
 
     If different entities apply,
-    such as a different session indicated by [`ses-<label>`](../99-appendices/09-entities.md#ses),
+    such as a different session indicated by [`ses-<label>`][SPEC_ROOT/appendices/entities.md#ses),
     or different acquisition parameters indicated by
-    [`acq-<label>`](../99-appendices/09-entities.md#acq),
+    [`acq-<label>`](SPEC_ROOT/appendices/entities.md#acq),
     then `run` is not needed to distinguish the scans and MAY be omitted.
   type: string
   format: index
@@ -311,10 +311,10 @@ space:
     The `space-<label>` entity can be used to indicate the way in which electrode positions are interpreted
     (for EEG/MEG/iEEG data)
     or the spatial reference to which a file has been aligned (for MRI data).
-    The `<label>` MUST be taken from one of the modality specific lists in
-    [Appendix VIII](../99-appendices/08-coordinate-systems.md).
+    The `<label>` MUST be taken from one of the modality specific lists in the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md).
     For example, for iEEG data, the restricted keywords listed under
-    [iEEG-Specific Coordinate Systems](../99-appendices/08-coordinate-systems.md#ieeg-specific-coordinate-systems)
+    [iEEG Specific Coordinate Systems](SPEC_ROOT/appendices/coordinate-systems.md#ieeg-specific-coordinate-systems)
     are acceptable for `<label>`.
 
     For EEG/MEG/iEEG data, this entity can be applied to raw data,
@@ -338,7 +338,7 @@ 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](../03-modality-agnostic-files.md#scans-file).
+    as described in [Scans file](SPEC_ROOT/03-modality-agnostic-files.md#scans-file).
   type: string
   format: index
 stain:
diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml
index 995b6731be..90aaf84586 100644
--- a/src/schema/objects/extensions.yaml
+++ b/src/schema/objects/extensions.yaml
@@ -42,7 +42,7 @@ bvec:
     Following the FSL format for the `bvec` specification, the coordinate system of
     the *b* vectors MUST be defined with respect to the coordinate system defined by
     the header of the corresponding `_dwi` NIfTI file and not the scanner's device
-    coordinate system (see [Coordinate systems](../99-appendices/08-coordinate-systems.md)).
+    coordinate system (see [Coordinate systems](SPEC_ROOT/appendices/coordinate-systems.md)).
     The most relevant limitation imposed by this choice is that the gradient information cannot
     be directly stored in this format if the scanner generates *b*-vectors in *scanner coordinates*.
 chn:
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index f1a41b3211..f7615ee7fc 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -68,7 +68,7 @@ AnatomicalLandmarkCoordinateSystem:
   display_name: Anatomical Landmark Coordinate System
   description: |
     Defines the coordinate system for the anatomical landmarks.
-    See [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"AnatomicalLandmarkCoordinateSystemDescription"`.
@@ -624,8 +624,8 @@ DigitizedHeadPointsCoordinateSystem:
   display_name: Digitized Head Points Coordinate System
   description: |
     Defines the coordinate system for the digitized head points.
-    See
-    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"DigitizedHeadPointsCoordinateSystemDescription"`.
@@ -725,8 +725,8 @@ EEGCoordinateSystem:
   description: |
     Defines the coordinate system for the EEG sensors.
 
-    See
-    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `EEGCoordinateSystemDescription`.
@@ -803,9 +803,9 @@ EchoTime:
     (please note that the DICOM term is in milliseconds not seconds).
     The data type number may apply to files from any MRI modality concerned with
     a single value for this field, or to the files in a
-    [file collection](SPEC_ROOT/99-appendices/10-file-collections.md)
+    [file collection](SPEC_ROOT/appendices/file-collections.md)
     where the value of this field is iterated using the
-    [`echo` entity](SPEC_ROOT/99-appendices/09-entities.md#echo).
+    [`echo` entity](SPEC_ROOT/appendices/entities.md#echo).
     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
@@ -932,8 +932,8 @@ FiducialsCoordinateSystem:
   description: |
     Defines the coordinate system for the fiducials.
     Preferably the same as the `"EEGCoordinateSystem"`.
-    See
-    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"FiducialsCoordinateSystemDescription"`.
@@ -996,9 +996,9 @@ FlipAngle:
     Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`.
     The data type number may apply to files from any MRI modality concerned with
     a single value for this field, or to the files in a
-    [file collection](SPEC_ROOT/99-appendices/10-file-collections.md)
+    [file collection](SPEC_ROOT/appendices/file-collections.md)
     where the value of this field is iterated using the
-    [`flip` entity](SPEC_ROOT/99-appendices/09-entities.md#flip).
+    [`flip` entity](SPEC_ROOT/appendices/entities.md#flip).
     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
@@ -1132,7 +1132,7 @@ HED:
   display_name: HED
   description: |
     Hierarchical Event Descriptor (HED) information,
-    see: [Appendix III](SPEC_ROOT/99-appendices/03-hed.md) for details.
+    see the [HED Appendix](SPEC_ROOT/appendices/hed.md) for details.
   anyOf:
     - type: string
     - type: object
@@ -1196,8 +1196,8 @@ HeadCoilCoordinateSystem:
   display_name: Head Coil Coordinate System
   description: |
     Defines the coordinate system for the head coils.
-    See
-    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `HeadCoilCoordinateSystemDescription`.
@@ -1636,7 +1636,7 @@ License:
   description: |
     The license for the dataset.
     The use of license name abbreviations is RECOMMENDED for specifying a license
-    (see [Appendix II](SPEC_ROOT/99-appendices/02-licenses.md)).
+    (see [Licenses](SPEC_ROOT/appendices/licenses.md)).
     The corresponding full license text MAY be specified in an additional
     `LICENSE` file.
   type: string
@@ -1689,7 +1689,8 @@ MEGCoordinateSystem:
   display_name: MEG Coordinate System
   description: |
     Defines the coordinate system for the MEG sensors.
-    See [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `"MEGCoordinateSystemDescription"`.
@@ -2010,7 +2011,7 @@ NumberShots:
     after the k-space center is sampled.
     Please see
     [`"NumberShots"` metadata field]\
-    (SPEC_ROOT/99-appendices/11-qmri.md#numbershots-metadata-field)
+    (SPEC_ROOT/appendices/qmri.md#numbershots-metadata-field)
     in the qMRI appendix for corresponding calculations.
   anyOf:
     - type: number
@@ -3301,8 +3302,8 @@ iEEGCoordinateSystem:
   display_name: iEEG Coordinate System
   description: |
     Defines the coordinate system for the iEEG sensors.
-    See
-    [Appendix VIII](SPEC_ROOT/99-appendices/08-coordinate-systems.md)
+    See the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md)
     for a list of restricted keywords for coordinate systems.
     If `"Other"`, provide definition of the coordinate system in
     `iEEGCoordinateSystemDescription`.
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index d705c9966e..5146907cdb 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -479,7 +479,7 @@ UNIT1:
     contain white salt-and-pepper noise that most segmentation algorithms will
     fail on.
     Therefore, it is important to dissociate it from `T1w`.
-    Please see [`MP2RAGE` specific notes](SPEC_ROOT/99-appendices/11-qmri.md#unit1-images)
+    Please see [`MP2RAGE` specific notes](SPEC_ROOT/appendices/qmri.md#unit1-images)
     in the qMRI appendix for further information.
 VFA:
   value: VFA
@@ -685,7 +685,7 @@ phase:
     Phase information associated with magnitude information stored in BOLD
     contrast.
     This suffix should be replaced by the
-    [`part-phase`](SPEC_ROOT/99-appendices/09-entities.md#part)
+    [`part-phase`](SPEC_ROOT/appendices/entities.md#part)
     in conjunction with the `bold` suffix.
   anyOf:
     - unit: arbitrary
diff --git a/src/schema/objects/top_level_files.yaml b/src/schema/objects/top_level_files.yaml
index 5583ddae4c..87b27e874f 100644
--- a/src/schema/objects/top_level_files.yaml
+++ b/src/schema/objects/top_level_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](../03-modality-agnostic-files.md#sessions-file) in case it changes over time.
+        [Sessions files](SPEC_ROOT/03-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`)
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index b5d57e2f96..c5abb23c85 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -35,12 +35,12 @@ MEGRecommended:
         For MEG scanners, this must be one of:
         `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
         `"ITAB"`, `"KRISS"`, `"Other"`.
-        See [Appendix VII](SPEC_ROOT/99-appendices/07-meg-systems.md) for
+        See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for
         preferred names.
     ManufacturersModelName:
       level: recommended
       description_addendum: |
-        See [Appendix VII](SPEC_ROOT/99-appendices/07-meg-systems.md) for
+        See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for
         preferred names.
     SoftwareVersions: recommended
     TaskDescription: recommended
diff --git a/tools/schemacode/bidsschematools/render.py b/tools/schemacode/bidsschematools/render.py
index f5a48a2875..eb2555693f 100644
--- a/tools/schemacode/bidsschematools/render.py
+++ b/tools/schemacode/bidsschematools/render.py
@@ -19,8 +19,8 @@
 logging.basicConfig(format="%(asctime)-15s [%(levelname)8s] %(message)s")
 
 # Remember to add extension (.html or .md) to the paths when using them.
-ENTITIES_PATH = "SPEC_ROOT/99-appendices/09-entities"
-GLOSSARY_PATH = "SPEC_ROOT/99-appendices/14-glossary"
+ENTITIES_PATH = "SPEC_ROOT/appendices/entities"
+GLOSSARY_PATH = "SPEC_ROOT/glossary"
 TYPE_CONVERTER = {
     "associated_data": "associated data",
     "columns": "column",
@@ -529,7 +529,7 @@ def make_entity_table(schema, tablefmt="github", src_path=None, **kwargs):
         File in which entities are described.
         This is used for hyperlinks in the table, so the path to the file
         should be considered from the location of out_file.
-        Default is '09-entities.md'.
+        Default is 'entities.md'.
 
     Returns
     -------
diff --git a/tools/schemacode/bidsschematools/tests/test_render.py b/tools/schemacode/bidsschematools/tests/test_render.py
index 6498be7ffb..1ea009414d 100644
--- a/tools/schemacode/bidsschematools/tests/test_render.py
+++ b/tools/schemacode/bidsschematools/tests/test_render.py
@@ -117,17 +117,17 @@ def test_make_entity_table(schema_obj):
 
     # Non-exhaustive list covering both value and index formats
     expected_entities = [
-        "[`acq-<label>`](./99-appendices/09-entities.md#acq)",
-        "[`ses-<label>`](./99-appendices/09-entities.md#ses)",
-        "[`sample-<label>`](./99-appendices/09-entities.md#sample)",
-        "[`task-<label>`](./99-appendices/09-entities.md#task)",
-        "[`acq-<label>`](./99-appendices/09-entities.md#acq)",
-        "[`ce-<label>`](./99-appendices/09-entities.md#ce)",
-        "[`trc-<label>`](./99-appendices/09-entities.md#trc)",
-        "[`stain-<label>`](./99-appendices/09-entities.md#stain)",
-        "[`rec-<label>`](./99-appendices/09-entities.md#rec)",
-        "[`dir-<label>`](./99-appendices/09-entities.md#dir)",
-        "[`run-<index>`](./99-appendices/09-entities.md#run)",
+        "[`acq-<label>`](./appendices/entities.md#acq)",
+        "[`ses-<label>`](./appendices/entities.md#ses)",
+        "[`sample-<label>`](./appendices/entities.md#sample)",
+        "[`task-<label>`](./appendices/entities.md#task)",
+        "[`acq-<label>`](./appendices/entities.md#acq)",
+        "[`ce-<label>`](./appendices/entities.md#ce)",
+        "[`trc-<label>`](./appendices/entities.md#trc)",
+        "[`stain-<label>`](./appendices/entities.md#stain)",
+        "[`rec-<label>`](./appendices/entities.md#rec)",
+        "[`dir-<label>`](./appendices/entities.md#dir)",
+        "[`run-<index>`](./appendices/entities.md#run)",
     ]
 
     for expected_entity in expected_entities: