• Fix: the Obsidian export (--obsidian / to_obsidian) no longer overwrites a user's own notes or .obsidian/ config when pointed at an existing vault (#1506). It wrote one note per node straight into the target dir and unconditionally replaced .obsidian/graph.json, so --obsidian-dir ~/my-vault could clobber a same-named note (Database.md) and the user's graph-view settings — silently, no backup. graphify now records the files it owns in a .graphify_obsidian_manifest.json and refuses to overwrite any pre-existing file it didn't create (skipping it with one aggregated warning); a re-run still updates graphify's own notes. The default graphify-out/obsidian output is unchanged.
• Fix: Java enum and annotation (@interface) declarations are now emitted as type nodes (#1512, thanks @oleksii-tumanov), so a field typed as an enum or a class annotated with a project annotation resolves to a real node instead of a dangling reference.
• Fix: Java generic parent relationships are no longer dropped (#1510, thanks @oleksii-tumanov) — class Foo extends Bar<T> / implements List<T> now emit the inherits/implements edge to the base type, with the type arguments as generic_arg references.
• Fix: the claude-cli backend no longer crashes with UnicodeDecodeError on Windows systems where claude.cmd emits GBK/cp936 bytes (#1505, thanks @nuthalapativarun) — both subprocess calls decode with errors="replace".
• Fix: graphify explain and graphify affected now resolve a query given as a source-file path even when the graph has multiple nodes from that file (#1503, thanks @behavio1). A path like app/api/route.ts tokenized to terms that matched no node, so explain returned "No node matching"; source-file paths are now indexed and matched exactly, and when several nodes share the file the lookup prefers the file-level node (the L1 node whose name matches the file). Trailing-separator handling is aligned between the two commands.
• Docs: clearer install/PATH guidance for uv tool install graphifyy on macOS (#1471, thanks @Patsch36). Two expected uv behaviors read as bugs: (1) after uv tool install, the graphify command lands in uv's tool bin dir (~/.local/bin), which a fresh macOS/zsh shell often doesn't have on PATH — the README now points to uv tool update-shell instead of implying uv always wires PATH; (2) uvx graphify … / uv tool run graphify … resolve the first word as a package and fail, because the package is graphifyy and graphify is only its console script — the docs now show uvx --from graphifyy graphify install. README install note + Troubleshooting only; no code change.
• Fix: imported type stubs with the same label no longer falsely merge across files when there is no project definition to rewire onto (#1462, thanks @jiangyq9). Two files that both from pathlib import Path and use Path as a type previously collapsed into one node; the referencing file is now kept as an internal disambiguator (origin_file) used only when splitting colliding ids, while source_file stays empty so a real project definition can still be rewired onto (the #1402 path is unaffected).
• Feat: resolve C# cross-file type references and extract enum/struct/record declarations (#1466, thanks @TheFedaikin). A new _resolve_csharp_type_references (the C# counterpart to the Java resolver) re-points dangling inherits/implements/references edges from no-source "shadow" stubs to their real definitions, disambiguating same-named types in different namespaces via the referencing file's using directives and enclosing namespace; ambiguous matches are refused rather than guessed. enum/struct/record types are now extracted as definitions so those references resolve too. Advances #1318 for C#.
• Fix: the Go AST extractor no longer creates phantom duplicate nodes for cross-file type references — the Go copy of ensure_named_node still used the older sourced-stub fallback; it now emits a sourceless stub like the other extractors, extending the #1402 fix to Go (#1500, thanks @TPAteeq).