chore: remove unused GSD agent scaffolding and its dangling references

[VibhavSetlur]

Summary

Removes AI-agent planning scaffolding that is tracked in the repository but referenced by nothing in the build, runtime, or test surface, plus the reference lines that would otherwise dangle.

No application behavior changes. No dependency, version, or source-code change.

What is removed

Item	What it is	Why it can go
.gsd/ (249 files)	"Get Shit Done" methodology planning scaffolding — roadmap, phases, milestones, agent task specs	Nothing under app/, lib/, components/, tests/, or .github/ reads it
.clauderules (18 lines)	GSD agent instruction file	Every path it points at is untracked (PROJECT_RULES.md, .agent/skills/, .agent/workflows/, .gemini/GEMINI.md) or removed here (.gsd/)
gsd-opencode	Orphan submodule gitlink (160000 4527186)	There is no tracked .gitmodules, so this submodule can never be initialized by anyone cloning the repo

Dangling references cleaned up

Every remaining mention, found with git grep -nE 'gsd|\.clauderules':

• .gitignore:74 — dropped .gsd/.opencode/
• INDEX.md — dropped the ## State and Planning section. Both of its rows were dead: .gsd/ is removed here, and .agent/ was never tracked (git ls-files .agent → 0 files).
• README.md:128 — dropped the .gsd/ROADMAP.md documentation entry point
• docs/DEVELOPER_GUIDE.md:4,53 — dropped two .gsd/STATE.md pointers, keeping the surrounding guidance
• eslint.config.mjs:17 — dropped the now-meaningless gsd-opencode/** ignore
• vitest.config.ts:11,22 — dropped gsd-opencode/** from test.exclude and coverage.exclude
• CHANGELOG.md — ### Removed entry under ## [Unreleased], per CONTRIBUTING.md

package-lock.json:5817 contains gsd inside a base64 integrity hash — false positive, untouched.

Deliberately NOT touched

• legacy/ — also untracked, and INDEX.md still links to a legacy/README.md that does not exist. Same class of problem, but a separate pre-existing issue; left for a follow-up so this diff stays one topic.
• INDEX.md rows linking to untracked AGENTS.md / PROJECT_RULES.md — those are intentionally-gitignored local agent files, same reasoning.
• Anything Solr, security, or dependency related.

Happy to fold the legacy/ cleanup in here if you'd rather have one sweep.

Verification

Run on a clean worktree of this branch (conda env modelseed-ui):

Check	Result
npm run lint	exit 0 — 0 errors, 16 pre-existing warnings
npx tsc --noEmit	exit 0
npm run test:run	exit 0 — 18 files, 145 passed (identical to the base; the removed vitest excludes matched no test files)
npm run build	exit 0 — compiled successfully
npm audit --omit=dev --audit-level=high	exit 1 — 1 high, nanoid GHSA-2v37-7h3g-55p8, inherited from the base branch and fixed by #230. Not caused by this PR; this PR does not touch package-lock.json.
git diff --stat <base>..HEAD -- package.json package-lock.json VERSION.md .env.example	empty
git grep -nE '\.gsd|gsd-opencode|clauderules' (excluding the changelog record)	no matches

Merge order

This is the third and last of three stacked PRs. It is based directly on staging, and git merge-tree confirms it merges cleanly with no conflicts against both of the others, so the order is a convenience rather than a hard requirement:

1. fix: clear nightly CI audit failure (nanoid 3.3.18) and group Dependabot updates — 3.1.1 #230 — security / Dependabot / 3.1.1 (fixes the nanoid advisory and turns CI green)
2. feat(biochem): Solr 9 compatibility, per-corpus endpoint configuration, and color-blind-safe atom mapping #231 — Solr 9 UI compatibility (3.4.0)
3. this PR — cleanup

Only overlap with the other two is CHANGELOG.md, and it is in a different section ([Unreleased] here vs. new release sections there).