feat: namespace MCP tools, drop content rehash, tune stopwords

[Abas-Tim]

Follow-up to #17 with the previously-deferred items:

• MCP tools renamed to urag_* (urag_search, urag_fetch_unit, urag_callers, ...) so they never collide with other servers; server instructions, skill doc, and tests updated. Harnesses that add their own server-name prefix will expose <server>_urag_*.
• _needs_reindex no longer content-hashes files whose size+mtime match stored values (any repo kind). Same-size-same-mtime edits are intentionally not detected by plain re-index runs; the watcher and forced rebuilds still catch real edits. Legacy rows without a hash are backfilled once.
• Definition-query stopword list expanded to ~90 common English words.

Verification

• 158 tests / 1 skipped; ruff clean; wheel+sdist build.
• Benchmarks (same 44 questions): no regressions (auto 0.947, hybrid 0.583, lexical 0.947, callers/transitive 1.000, references 0.928); tokens slightly down (hybrid 701->697, callers 940->937).
• MCP stdio probe confirms the 17 renamed tools.