fix: resolve absolute DB path to prevent SQLITE_CANTOPEN on CWD change

[cynthiateeters]

Summary

Fixes #31.

The server opened context.db using a bare relative path, so SQLite resolved it against the process's CWD at startup. Users running node dist/index.js directly (as the README instructed) bypassed the bin/mcp-memory-keeper wrapper that guards against this, causing SQLITE_CANTOPEN whenever the parent process started with a different CWD.

Changes

src/index.ts

• Resolves DB path to an absolute location: $DATA_DIR/context.db (with path.resolve() to guard against a relative DATA_DIR) or ~/mcp-data/memory-keeper/context.db as the default fallback
• Creates the data directory with mkdirSync({ recursive: true }) if it does not exist
• Emits a stderr warning with the exact cp command when a context.db is found in CWD but the server is opening from a different path (migration warning — no auto-copy per discussion in Server crashes with SQLITE_CANTOPEN when parent process CWD changes #31)

README.md

• Line 177: updated from-source install command to use bin/mcp-memory-keeper instead of node dist/index.js
• Added Upgrading section documenting the new default DB path and migration steps

Tests

• server-initialization.test.ts: passes DATA_DIR: tempDir in spawn env so the test reflects the new absolute-path behavior
• git-integration.test.ts: updated hardcoded 'master' branch assertion to 'main' (pre-existing failure unrelated to this fix)

Test plan

• All 1185 tests pass (66 suites)
• Verified manually:
  • DATA_DIR=/tmp/test node dist/index.js → DB created at /tmp/test/context.db ✅
  • HOME=/tmp/fake-home node dist/index.js → DB created at /tmp/fake-home/mcp-data/memory-keeper/context.db ✅
  • DATA_DIR=./relative node dist/index.js → resolves to absolute path ✅
  • Migration warning fires with exact cp command when legacy context.db detected in CWD ✅
  • bin/mcp-memory-keeper wrapper continues to work correctly ✅

[mkreyman]

Nice work — the core fix is solid. A few things to address before merge:

Must fix

1. Three tests still pass MCP_DB_PATH which the server never reads

Lines 70, 190, 268 in server-initialization.test.ts pass MCP_DB_PATH: dbPath, but src/index.ts only reads DATA_DIR. These tests don't actually control the DB path — post-merge they'll silently write to ~/mcp-data/memory-keeper/ during test runs. Should be DATA_DIR: tempDir like the second test you already fixed.

2. No error handling on fs.mkdirSync

If mkdirSync fails (e.g., permission denied), the server crashes with a raw Node.js stack trace before reaching the DatabaseManager. Since the whole point of this PR is to prevent cryptic startup crashes, a try/catch with an actionable message would be consistent:

try {
  fs.mkdirSync(dataDir, { recursive: true });
} catch (err) {
  console.error(
    `[memory-keeper] FATAL: Cannot create data directory "${dataDir}": ${(err as NodeJS.ErrnoException).message}\n` +
    `Set DATA_DIR to a writable location or create the directory manually.`
  );
  process.exit(1);
}

Should fix

3. Version reference says "v0.13.0+" but this will ship as 0.12.x

The Upgrading section header says ### Database path change (v0.13.0+) — should match whichever version this actually releases under.

---

Happy to push fixup commits for these if you'd like, or let me know if you'd prefer to address them yourself.

[cynthiateeters]

Thanks for the offer to keep working the issue. I haven't done any open source contributing for a while and it's been fun to get back into it. I also use real-world scenarios like this with my JavaScript students — I stress that they need to work in a real developer environment with real tools, so being able to point to my own PRs as examples makes that lesson land better.

The try/catch on mkdirSync is a great catch — as someone who teaches JavaScript best practices around error handling, I especially appreciate that one.

I'll address all three items.

[mkreyman]

All three items addressed cleanly. Thanks for the thorough work, @cynthiateeters!

[cynthiateeters]

You're very welcome 😎, @mkreyman