fix(manifest): register brainpy-state and brainx-general-guard, relocate NEST branch

[chaoming0625]

Why CI was failing

Every recent run of Agent Skills validation failed at the Verify the skill manifest step:

manifest.json does not match the skill directories.
Manifest:    brainevent brainstate brainunit brainx-install
Directories: brainevent brainpy-state brainstate brainunit brainx-general-guard brainx-install

skills/brainpy-state/ and skills/brainx-general-guard/ were added without matching manifest.json entries. The workflow compares the sorted manifest array against the sorted directory listing and fails on any difference in either direction (AGENTS.md rule 6). The failure happened before the per-skill validation step ever ran, so no skill was actually being validated in CI.

The same omission left both directories out of package.json files (rule 7). CI does not check that, so it was a latent packaging bug: manifest.json would have declared skills the published tarball did not contain, and installation/lib/bundle.js rejects undeclared directories under skills/.

Changes

1. Register the two skills — manifest.json and package.json files. This is the CI fix.

2. Relocate the NEST-compatible branch — skills/brainpy-state/NEST-compatible/ violated rule 1, which permits only references/, scripts/, and agents/ beneath a skill. Moved to references/nest-compatible/, flattening its inner references/ into the grouping directory and keeping scripts/ alongside, mirroring the existing references/brainstate-dynamics/ layout.

Routing links in the branch are now skill-root-relative, matching SKILL.md and references/brainstate-dynamics/. This removes a real hazard: nest-workflow.md routed to `references/model-library.md`, which after the move would resolve against the skill's own references/ directory instead of the NEST branch. Inbound links in SKILL.md and references/component-selection.md, plus the layout tree, nested-branch table, and script paths in plan.md, were updated to match.

No skill prose or API content changed — the relocation is paths only.

Verification

All six skills validate:

$ for d in skills/*/; do python -c 'from skills_ref.cli import main; main()' validate "${d%/}"; done
Valid skill: skills/brainevent
Valid skill: skills/brainpy-state
Valid skill: skills/brainstate
Valid skill: skills/brainunit
Valid skill: skills/brainx-general-guard
Valid skill: skills/brainx-install

Manifest check passes, and every skill now has only rule 1 subdirectories:

manifest matches: brainevent brainpy-state brainstate brainunit brainx-general-guard brainx-install
skills/brainevent/:           references
skills/brainpy-state/:        references
skills/brainstate/:           agents references scripts
skills/brainunit/:            references
skills/brainx-general-guard/: references
skills/brainx-install/:       references

Every backticked .md/.py routing target under skills/brainpy-state/ was resolved against the filesystem; all now exist. The only unresolved names are upstream NEST example filenames quoted inside script docstrings, which are prose, not routing links.

Pre-existing issue, not fixed here

references/brainstate-dynamics/brain-dynamics-event-driven-operators.md has a "## Used by" block listing references/brainstate-dynamics/dynamics-and-integration.md and references/brainstate-dynamics/brain-dynamics-snn-workflows.md. Neither file exists in this skill; they look like skills/brainstate/ paths. Present in HEAD before this branch and left untouched.