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

Author: StackMemory Bot (CLI)

.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/

.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