chore: reorganize root and fix session tests (#11)

* feat(conductor): GitButler virtual branch mode for workspace management

* fix(conductor): state filter + labels flatten for issue dispatch

* fix(linear): flatten labels in getIssues response

* feat(cross-search): multi-database frame search across projects (STA-480)

- Add CrossProjectSearch engine with FTS5/BM25 ranking across N databases
- Project registry (~/.stackmemory/projects.json) with CRUD + auto-discovery
- Read-only SQLite connections for safety, LIKE fallback for non-FTS databases
- 4 MCP tools: sm_cross_search, sm_cross_discover, sm_cross_register, sm_cross_list
- CLI: `stackmemory search --all-projects "query"` for cross-project search
- 17 tests: registry CRUD, multi-db FTS5 search, ranking, LIKE fallback, graceful skip

* feat(shared-state): add canonical instance coordination

* feat: add deterministic harness smoke tooling

* docs: add design principles architecture note

* chore: update gepa baselines and clean GitButler hooks

* fix(conductor): harden lane mode cleanup

* chore: reorganize root for clarity

Consolidate duplicate docs, relocate wandering files, and tighten
.gitignore for agent scratch dirs.

- Move SPEC.md, RELEASE_NOTES.md, tomorrow.md, vision.md to docs/
  (replacing stale docs/ copies with the up-to-date root versions)
- Move mcp_review_config.json to config/
- Untrack .lint-fix-log.json (ephemeral lint artifact)
- Delete stale .tsbuildinfo-* and .lint-errors.log
- Ignore agent scratch dirs (.ralph/, .swarm/, .bjarne/, .entire/,
  .opencode/, .git.backup/) and local trees (archive/, site/,
  voyager/, plugins/)
- Update README.md Vision link to docs/vision.md

* fix(test): mock canonicalStateStore in session tests

Session tests mocked fs/promises but not the canonical-store module.
The canonicalStateStore singleton inherited the mocked fs, causing
pathExists to return true while readFile returned undefined — crashing
JSON.parse. Mock the entire canonical-store module with stubs for
upsertSession, appendEvent, and endSession.

---------

Co-authored-by: StackMemory Bot (CLI) <bot@stackmemory.ai>
Co-authored-by: GitButler <gitbutler@gitbutler.com>

Author: 3 people

.gitignore

@@ -135,3 +135,22 @@ scripts/gepa/results/scores.jsonl
 scripts/gepa/state.json
 scripts/gepa/results/
 scripts/gepa/generations/
+
+# Agent tool working dirs (untracked, per-tool scratch)
+.ralph/
+.swarm/
+.bjarne/
+.entire/
+.opencode/
+
+# Local backups and lint artifacts
+.git.backup/
+.lint-errors.log
+.lint-fix-log.json
+.lint-fix-log.*.json
+
+# Local scratch / generated trees
+archive/
+site/
+voyager/
+plugins/

.husky/pre-commit

@@ -10,4 +10,5 @@ elif [ -d "$HOME/.nvm/versions/node" ]; then
 fi
 
 npx lint-staged
+bash scripts/determinism-pre-commit.sh
 npm run build

.lint-fix-log.json

@@ -423,7 +423,7 @@ Options: `--until`, `--until-not`, `--until-empty`, `--until-non-empty`, `--unti
 - [Development Guide](./docs/DEVELOPMENT.md) — Contributing and development
 - [Architecture](./docs/architecture.md) — System design
 - [API Reference](./docs/API_REFERENCE.md) — API documentation
-- [Vision](./vision.md) — Product vision and principles
+- [Vision](./docs/vision.md) — Product vision and principles
 - [Status](./docs/status.md) — Current project status
 - [Roadmap](./docs/roadmap.md) — Future plans