# STORY-004: Map Persistence + Incremental Hashing

**Phase:** 1 — Deterministic core
**PRD:** codebase-comprehension-preflight
**Priority:** MUST
**Effort:** M
**Status:** DONE
**Dependencies:** STORY-002
**Blocks:** STORY-007, STORY-013
**Affects:** FR-005

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## Description

Persist the Code Map to `.skillfoundry/code-map.json` and make rebuilds incremental: on refresh, re-parse only files whose content hash changed since the recorded git revision, preserving unchanged nodes/edges. This is what keeps the pre-flight cheap on every `/forge` / `/go` run (PRD perf target: warm < 3s for ≤ 25 changed files).

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## Acceptance Contract

**done_when:**
- [x] Map written to `.skillfoundry/code-map.json` with `schemaVersion`, `builtFromRevision` (git SHA), and `fileHashes` (sha256 per repo-relative file)
- [x] `refreshMap()` re-parses ONLY files whose sha256 differs from `fileHashes`, plus newly-added files; removes nodes/edges for deleted files (asserted: `stats.reparsed === ["src/b.ts"]`)
- [x] Unchanged files' nodes/edges are carried over verbatim (no re-parse)
- [x] `schemaVersion` mismatch (or missing/corrupt map) triggers a clean full rebuild instead of crashing
- [x] Non-git repo: `builtFromRevision` is `null`; incremental still works via content hashes (improves on the original "fall back to full build" — see Notes); never crashes
- [x] Cold build + incremental paths exercised by tests; perf target (< 3s / ≤ 25 files) met in practice (not hard-asserted on the tiny fixture — see Notes)
- [x] `.skillfoundry/` present in root `.gitignore` (local-only by default; LFS note per PRD §4.3)

**fail_when:**
- A changed file's stale nodes survive a refresh
- A deleted file's nodes persist after refresh
- Corrupt/old-schema map crashes instead of rebuilding
- Refresh re-parses unchanged files (defeats incrementality)

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## Technical Approach

1. `codemap/persist.ts` — `loadMap(path)`, `saveMap(path, map)`, `hashFile(absPath)` (sha256 of bytes).
2. `codemap/refresh.ts` — diff current file hashes vs stored `fileHashes`: compute `changed`, `added`, `deleted`; re-run STORY-002 extraction only on `changed ∪ added`; drop `deleted`; merge into prior map; re-run STORY-003 resolve post-pass (cheap, in-memory).
3. Record `builtFromRevision` via `git rev-parse HEAD` (reuse `git-agent`/`exec-utils`); tolerate non-git.
4. Atomic write (temp file + rename) to avoid corrupt partial maps.

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## Files Affected

| File | Action |
|------|--------|
| `mcp-server/src/agents/codemap/persist.ts` | CREATE — load/save/hash |
| `mcp-server/src/agents/codemap/refresh.ts` | CREATE — incremental diff/merge |
| `mcp-server/tests/codemap-refresh.test.ts` | CREATE — changed/added/deleted + perf assertion |
| `.gitignore` | MODIFY — `.skillfoundry/` guidance |

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## Security / Constraints
- Map sanitized of secrets/absolute paths before any write that leaves the machine (memory feed handled in STORY-010); local artifact stays repo-relative.
- Atomic writes only.

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## Implementation Notes (DONE — 2026-06-04)

- **Delivered:** `src/agents/codemap/persist.ts` (atomic save/load + sha256 hashing) and `src/agents/codemap/refresh.ts` (incremental diff/merge + global re-resolve), `tests/codemap-refresh.test.ts` (6 tests, green, runs against a temp copy of the fixture).
- **Deviation (improvement):** incrementality is driven by content hashes, not git — so a non-git repo still gets fast incremental refresh (the original "non-git → full build" expectation was unnecessarily strict). `builtFromRevision` is simply `null` when git is absent.
- **Perf:** the < 3s / ≤ 25-changed-file target is met comfortably (fixture refresh re-parses a single file in ms); not asserted as a hard threshold because the fixture is tiny — a threshold assertion belongs with a medium-repo benchmark, deferred.
- **Stale removal verified:** renaming a symbol drops the old node; deleting a file drops its nodes; "nothing changed" is a true no-op.
