docs: comprehensive AGENTS.md domain coverage#30
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Each domain's contract (parsed by src/runtime/contracts.ts) now documents every non-test source file with its purpose and cross-file/cross-domain relationships, instead of only the 4-5 most central files. Biggest change is src/runtime/AGENTS.md (~45 files grouped by subsystem: state machine, contracts, plan/task tools, artifacts, recovery flows, TDD, git sync, status/UI, timers, misc). Also touches src/storage, src/instructions, src/settings, src/session, src/AGENTS.md, instructions/AGENTS.md, and .github/AGENTS.md. src/git, src/guard, src/worktree, src/project-local, and the root AGENTS.md were already adequate and left untouched. Verified with `npx vitest run src/runtime/contracts.test.ts` (schema parses without errors for all 14 AGENTS.md files) and full `npx vitest run` (378/378 passing). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…lings Adds short inline comments at the source of invariants that were only documented (if at all) in AGENTS.md, so the constraint is visible right where it could be silently broken: atomic-write guarantees in storage/fs.ts, the state.json normalization blast radius, the dual-gate tool-policy<->stage-behavior coupling (guard + runtime sides), strict stage/step ordering with recovery as the sole exception, the AGENTS.md-only write restriction in contracts.ts, the three-layer instructions merge order, settings worktree-field precedence, worktree path/gitignore/git-watcher couplings, and the session header version contract in handoff.ts. No behavior changes - comments only. Verified with `npx vitest run` (378/378 passing), `npx tsc --noEmit` (clean), and `npx biome check` (clean) on all touched files. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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