fix(dir): store the project index in .codegraph/ instead of .codegraph-vba/

[ardelperal]

Closes #324

What changes

• The default per-project data directory is now .codegraph/ (src/directory.ts), so init, status, uninit and the MCP projectPath walk-up all use the path upstream CodeGraph and the agent harness expect.
• isCodeGraphDataDir goes back to the upstream shape. Its .codegraph-* prefix match still covers a legacy .codegraph-vba/, so a stale one in a consumer repo is never indexed or watched.
• Tests, README, CLAUDE.md, docs and scripts now use .codegraph/ instead of .codegraph-vba/.
• New tests: the default init writes .codegraph/codegraph.db and never creates .codegraph-vba/, and .codegraph-vba is still recognized as a data dir.
• CHANGELOG [Unreleased] has a Breaking Changes entry: existing projects must run init again.

Deliberately untouched

• Binary and package names (codegraph-vba, @aroman22/codegraph-vba): out of scope per the issue.
• The npm staging-dir cleanup (.codegraph-vba-<hash> in upgrade/ and postinstall-cleanup.js): those are npm install dirs, not the project index.
• Archived openspec/ notes, historical CHANGELOG entries and the benchmark record in docs/vba-extraction-perf.md, which record paths as they were at the time.
• No automatic migration of an existing .codegraph-vba/ (out of scope per the issue).

Verification

• npm run build passes.
• Passed locally: foundation, daemon-, exclude-config, vba-targets-config, dump-index-schema, external-integration-doc, extraction-vba-, resolution, upgrade.
• 2 codegraph_init tests in mcp-tools-lifecycle fail on my machine because a dependency is missing (fast-wrap-ansi for @clack/core), and more of them fail against main. CI is the source of truth here.

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