docs(changelog): record #1894(PR-1) #1916 #1915 #1912 in unreleased 0.9.17

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -4,6 +4,12 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 
 ## 0.9.17 (unreleased)
 
+- Fix: `--mode deep` is now effective over a warm cache instead of a silent no-op (#1894). The semantic cache is namespaced by mode (`semantic` vs `semantic-deep`) so a shallow-cached file no longer satisfies a deep run; `graphify extract` gains `--force` (and honors `GRAPHIFY_FORCE`) to bypass the incremental gate and the cache read; and a deep incremental run widens its dispatch to the full live doc set so the deep namespace actually gets populated. Cache prune/clear now sweep both namespaces so the deep cache can't accumulate orphans. (The skill-side flow that passes the mode through is a follow-up; the CLI is complete and backward compatible — the new `mode` argument defaults to the existing behavior.)
+- Fix: the semantic cache no longer persists dangling edges/hyperedges (#1916). When a node group was skipped on write (out-of-scope per the batch guard, or a ghost `source_file`), edges/hyperedges in the kept groups that referenced those never-written nodes were saved anyway and re-surfaced on every cache replay. Those references are now pruned at write time (gated on the scoping allowlist, so unscoped callers are unchanged), and `build_from_json` validates hyperedge members against the node set so a dangling hyperedge can't reach `graph.json` even from a live extraction.
+- Fix: `graphify update`/watch no longer produces a bloated graph by double-representing documents (#1915). `_rebuild_code` AST-quick-scanned Markdown/doc files and then preserved their existing semantic (LLM) nodes on top, so each doc appeared twice (a real corpus came out ~4x). A doc that already has semantic nodes in the graph is no longer AST-quick-scanned (its semantic nodes are the sole representation), while a doc with no semantic layer still gets the structural quick-scan; incremental rebuilds now preserve a doc's semantic nodes instead of evicting them, and previously-bloated graphs self-heal on the next full rebuild.
+- Fix: `.cjs` (explicit CommonJS) files are now recognized as code and parsed with the JavaScript grammar (#1912, thanks @Kookwater). The extension was half-registered (present in some internal maps but missing from the classification and dispatch sets), so `.cjs` files were silently dropped.
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 - Fix: files that become excluded (`.graphifyignore`/`.gitignore`/`--exclude`) are now pruned from both the graph and the manifest instead of lingering (#1908 / #1909). Two coupled gaps: `save_manifest` retained any prior row that still existed on disk (disk-existence, not scan-membership), so an excluded-but-present file was reported as `deleted` on every run; and the incremental prune set was derived from the manifest alone, so a newly-excluded file's stale nodes carried forward from the existing `graph.json` were never removed (the state every 0.9.16 graph is in). Now the incremental prune set also derives from the existing graph's own `source_file`s minus the post-exclude corpus (in-root only), `save_manifest` prunes rows outside the full scan corpus, and `detect_incremental` distinguishes truly-deleted files from excluded-but-present ones (which are no longer misreported as deleted).
 - Fix: PostgreSQL PL/pgSQL functions are no longer silently dropped (#1910). `CREATE FUNCTION ... LANGUAGE plpgsql AS $$...$$` with `OUT` params, tagged dollar-quotes, or procedural body statements parses as a tree-sitter `ERROR` node, which the SQL extractor skipped entirely. It now recovers the function/procedure name from an ERROR node via the same regex-fallback pattern the extractor already uses elsewhere, so the function node and its `contains` edge are kept (the unparseable body is left opaque) and surrounding statements are unaffected.