Issues filed for each. Failing tests added before fixes per CLAUDE.md.

- #bug2: tools called during scan-in-progress now append a "scan still in
  progress" hint when results look empty/unindexed. Pre-fix: a brand-new MCP
  server returned 0 results / "file not indexed" with no indication that the
  scan was still running, so agents took those answers as authoritative.
- #bug5: codedb_read detects binary files (NUL byte in first 8KB) and stubs
  the response with a hash + size line. Pre-fix: raw bytes including NULs
  got dumped into JSON content, corrupting downstream consumers and
  burning tokens on unreadable noise.
- #bug6: codedb_read now errors explicitly when line_start < 1, line_end < 1,
  or line_start > line_end. Pre-fix: invalid ranges silently returned an
  empty body so agents read it as "file is empty in that range".
- #bug7: codedb_search rejects empty query and non-positive max_results.
  Pre-fix: malformed args returned "0 results" — indistinguishable from a
  correct query that genuinely had no hits.
- #bug11: codedb_bundle marks isError=true when no op succeeded. Pre-fix:
  the envelope reported success while per-op error markers were buried in
  the body — agents thought the bundle ran fine.
- #bug10: codedb_index schema description now says "FOLDER (not a file)" so
  the directory-only requirement is discoverable from the schema.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>