v0.3.0

Added

• Before/after code-graph diff: graphtrail diff --before <db> --after <db> [--json] compares two indexed databases into added/removed/changed symbols and added/removed call edges, opening both read-only. Nodes key on (file_path, qualified_name, kind), so a symbol that only moves lines is not a spurious remove+add. The compact JSON output is built for attaching structural deltas to CI or agent-run receipts. (#10)
• MCP diff tool: the same before/after comparison over the MCP surface, taking explicit before/after database paths. (#12)
• Per-symbol body hashes (schema v3): a body edit that keeps the same signature and line span is now reported as changed instead of slipping through invisibly. Changed nodes carry a previous block with the before-side signature and start line, and the diff summary adds added_edges_line_insensitive / removed_edges_line_insensitive so a pure line shift reads as zero structural churn alongside the exact raw counts. Existing v2 databases upgrade in place with a one-pass reindex on the next sync. (#15)
• Extractor fingerprints (schema v4): each language extractor declares a version fingerprint recorded per file, and the incremental-sync skip check compares it alongside the content hash. Changing an extractor re-extracts exactly that language's files on the next sync, with no forced full-reindex migrations. (#17)
• MCP refresh parameter on the query tools (search, callers, callees, impact, context, file_neighbors, stats): opt-in incremental sync before answering, fail-open with a note if the sync cannot run. Queries themselves stay on read-only connections. (#17)
• graphtrail doctor: the freshness contract. Reports tool and schema versions, last-sync age, pending change counts (new / changed / deleted / fingerprint-stale files), and ignored-entry counts, then verdicts FRESH, STALE, or NEEDS-MIGRATION with exit codes 0/1/2 for scripting. Also exposed as an MCP tool, deliberately without refresh. (#18)

Changed

• Sync respects .gitignore in git repositories (including nested and .git/info/exclude), and files that become ignored are removed from the index on the next sync, so polluted databases clean themselves. Non-git roots keep the hardcoded skip list, which now also covers bare venv. Hidden paths are still indexed. One real-world graph went from 2,955 files (2,803 of them site-packages noise) to 152. (#16)
• First index of a git repository ensures .graphtrail/ is in .gitignore, idempotently. (#17)

Fixed

• The diff JSON contract, edge-identity behavior, and read-only guarantees are locked by regression fixtures: a full golden test for the JSON shape, a line-shift fixture for edge churn, a body-only fixture, and CLI tests asserting missing-database errors and unmutated inputs. (#14)