fix(knowledge-registry): surface incomplete scans and untracked discovery (AGT-3490)

[unohee]

Closes AGT-3490.

What

• getRecentlyChangedFiles now also enumerates untracked files (git ls-files --others --exclude-standard -z), so incremental graph refresh discovers newly created files that no commit has seen yet.
• scanRepository (entity scanner) and BS detector report an explicit incomplete flag + incompleteReasons[] when depth limits, scan timeouts, the file cap, or the size-based file exclusion truncate coverage — the omission is a result, not silence.
• entityWarnings GraphQL query enforces a request-wide result budget of 200 (offset+limit window must fit), and the store clamps offset on warning/tag queries so a huge offset can no longer bypass the page cap.
• Regression tests for each behavior; full src/registry+src/knowledge suite green (93 tests), typecheck clean.

DoD mapping

• New untracked source files are discovered by incremental refresh (src/knowledge/untrackedDiscovery.test.ts)
• Scan results explicitly indicate incompleteness caused by depth or size limits (src/registry/incompleteCoverage.test.ts)
• Regression coverage verifies both omission classes (oversized file, depth limit)
• entityWarnings obey a total request-wide result budget (src/registry/entityWarningsBudget.test.ts)

Verification

• npm run typecheck — 0 errors
• vitest src/registry + src/knowledge — 10 files, 93 passed
• oxlint on touched files — 0 warnings