This PR splits the tractography section from the diffusion derivatives
document, so that #5 is easier to merge.
The new ``05-diffusion-derivatives-tractography.md`` file will remain
orphaned, but kept there as a base for the time we tackle tractography.
It shouldn't be merged into the derivatives branch until it is ready.

[FIX] Split out tractography

- More clarity of distinction between requisite and optional files in output directory.
- Try using 3 spaces rather than 4 in non-code indentation; partly to try to get tables within dot point lists to render correctly, partly to improve editor software syntax highlighting.

- Various small re-wordings.
- Slightly more use of hyperlinks.
- Short introductions to "parameter terminology" and "data representations" sections.
- Be more explicit about normalised vs. non-normalised 3-vectors, so that structure more clusely mimics that of description of spherical coordinate representation.
- Rename hyperlink names to "parameter terminology" section to better separate from later "intrinsic / extrinsic model parameters" sections.

Based on suggestion in #5. If all model intrinsic parameters are incorporated into a single file, rather than dropping the "_parameter-<param>" field, instead enforce that parameter name "all" be used.

When introducing the file naming convention, give an example of the "_<model>" field.

Re-arranged descriptions of intrinsic and extrinsic model parameters within the file naming section, and corrected a discordance in one dot point that was using an intrinsic model parameter filename path but discussing extrinsic model parameters.

Provide information on specification of orientation data after the various models and model parameters have been explained.

[ENH] Restructuring of DWI derivatives

Revised based on MRtrix3/mrtrix3#1635.
Manual merge / cherry-pick of: c653985, 8b27828, c653985, ebbf0d3, d7b4731, 99e92e0, 6bfc784 due to unresolvable conflict in #8.

[FIX] Formatting conformity to pass CI

Conflicts:
	src/05-derivatives/05-diffusion-derivatives.md

Co-authored-by: Ariel Rokem <arokem@gmail.com>

- FSL bedpostx command fibre orientations stored as spherical coordinates are confirmed to use the "bvec" reference frame.
- Enforcing azimuth angle to obey the right hand rule about the zenith axis would necessitate direct modification of image intensities from bedpostx outputs to store. Therefore it would be preferable to instead define the sign of the azimuth angle based on the direction of the second reference axis.
Closes #95.
Closes #94.

Conflicts:
	src/derivatives/05-diffusion-derivatives.md

DWI models: Define "bvec" orientation reference

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v4...v5)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

… with 5 updates

Bumps the actions-infrastructure group with 5 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [actions/checkout](https://github.com/actions/checkout) | `5` | `6` |
| [actions/upload-artifact](https://github.com/actions/upload-artifact) | `4` | `5` |
| [actions/download-artifact](https://github.com/actions/download-artifact) | `5` | `6` |
| [actions/setup-node](https://github.com/actions/setup-node) | `4` | `6` |
| [actions/setup-python](https://github.com/actions/setup-python) | `5` | `6` |



Updates `actions/checkout` from 5 to 6
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

Updates `actions/upload-artifact` from 4 to 5
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v4...v5)

Updates `actions/download-artifact` from 5 to 6
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v5...v6)

Updates `actions/setup-node` from 4 to 6
- [Release notes](https://github.com/actions/setup-node/releases)
- [Commits](actions/setup-node@v4...v6)

Updates `actions/setup-python` from 5 to 6
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/upload-artifact
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/download-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/setup-node
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-infrastructure
...

Signed-off-by: dependabot[bot] <support@github.com>

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 7 to 8.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v7...v8)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-version: '8'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

…codecov/codecov-action-5

chore(deps): bump codecov/codecov-action from 4 to 5

…astral-sh/setup-uv-7

chore(deps): bump astral-sh/setup-uv from 6 to 7

…peter-evans/create-pull-request-8

chore(deps): bump peter-evans/create-pull-request from 7 to 8

…ructure-f2d4b981e8

…actions-infrastructure-f2d4b981e8

chore(deps): bump the actions-infrastructure group across 1 directory with 5 updates

Conflicts:
	src/derivatives/05-diffusion-derivatives.md

Use of "order" has been adopted across the documentation.

- Rename exemplar data and metadata files encoding the FSL bedpostx ball-and-sticks model from "_model-bs" to "_model-ballsticks" to avoid negative acronym connotation.
- Rename permissble value for "Reference" metadata from "bvec" to "fsl": this axis reference convention is not specific to the "bvec" file format but is a convention utilised throughout the FSL software.

New appendix page: spherical harmonics

Conflicts:
	src/derivatives/05-diffusion-derivatives.md

BEP016: Renaming relevant to FSL