Remove stale 'stub' / TODO comments on already-implemented modules

[amondnet]

Summary

Several modules carry "Minimal stub" / TODO(integration) / "throwing stub" comments that are stale — the code is fully implemented. These mislead readers (and audits) into thinking work is incomplete. Pure comment cleanup, no behavior change.

Stale markers to remove/update

• src/types.ts:2 — // Minimal stub — full implementation lands in Unit 1. → file is fully implemented (chunkToDict, chunkFromDict, searchResultToDict, …).
• src/utils.ts:2 — // Minimal stub — full implementation lands in Unit 3. → fully implemented (isGitUrl, resolveChunk, formatResults, …).
• src/cli.ts:8 — // TODO(integration): replace stub when sibling modules land → all sibling modules are imported and real.
• src/indexing/index.ts:7-13 — header says fromGit: stub (T005) and loadFromDisk: throwing stub (T007), but both are fully implemented (fromGit at :196, loadFromDisk at :389). Update the "Wiring status" block.

Out of scope

The genuine functional stubs are tracked separately:

• dense.ts fake embeddings (dense.ts ships a stub Model2Vec — semantic search uses fake embeddings #26)
• search.ts ranking integration (search.ts uses inline ranking stubs — ranking/ modules implemented but never wired in #27)
• ALL_LANGUAGES empty set (AST chunking never runs — core.ts ALL_LANGUAGES is an empty stub set #28)

Acceptance criteria

• Stale stub/TODO comments above removed or corrected to reflect implemented state.
• No code/behavior changes; bun run typecheck + bun test still green.