fix(extraction): index files reached through in-root symlinks that point outside the repo (#935) (#956)

The directory walk deliberately follows an in-root symlink whose target
lives outside the repo root (the standard Dota custom-game layout, where
`game/` and `content/` link into the SDK tree) and enumerates the files
under it. But the read path then rejected every one of them via the
strict symlink-escape guard, logging `Path traversal blocked in batch
reader` and indexing nothing — discovery and the reader disagreed.

Add an opt-in `allowSymlinkEscape` to validatePathWithinRoot that waives
only the realpath-escape rejection (the lexical `../` guard still
applies) and pass it at the three indexing read sites (batch reader,
indexFile, indexFileWithContent). The content-serving sinks
(ContextBuilder, MCP tools) keep the strict guard, so this stays inside
the #527 model: indexing now follows the symlink, getCode still refuses
to serve out-of-root contents.

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

CHANGELOG.md

@@ -49,6 +49,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 - A git worktree of a submodule is no longer indexed as a duplicate copy of that submodule's code. CodeGraph already skips ordinary worktrees (a second working view of a repo it indexes), but a worktree created *from a submodule* — common in monorepos that check submodules out into worktrees for parallel feature work — was mistaken for a genuine embedded repo and swept in, duplicating every symbol it shared with the real submodule checkout (one report had ~28% of its index as duplicates, inflating both query results and the database). These submodule worktrees are now recognized and skipped, while the submodule's own checkout stays indexed as distinct code. Thanks @charlesxu2026-ship-it. (#945)
 - A C++ class or struct annotated with an export/visibility macro — `class MYLIB_EXPORT Foo : public Bar { … }`, the common DLL-export / visibility pattern in headers — is no longer mis-indexed as a function spanning the whole class body. Not knowing the macro is a macro, the parser read it as a type and the whole declaration as a function, so the class surfaced as a phantom `function` that showed up as a false caller in `codegraph callers`, `codegraph impact`, and blast-radius analysis, and skewed symbol counts. CodeGraph now recognizes this misparse and drops the bogus node. Thanks @spwlyzx. (#946)
 - `codegraph status` no longer reports phantom pending changes for files CodeGraph deliberately keeps out of the index — a tracked file inside a committed dependency dir (a checked-in `vendor/` or `node_modules/`), or a tracked file under a `.gitignore`d directory. A full index correctly excludes these, and `codegraph sync` never indexes them, but the fast change-detector behind `codegraph status` flagged every edit to such a file as "modified" (and a new one as "added") — so the pending-changes count never cleared no matter how many times you synced. Change detection now applies the same ignore rules the full index does, so `status` agrees with `sync`, and tools built on CodeGraph's change-detection API get the same corrected list. (#766)
+- Files reached through a symlinked directory that points outside your project now index instead of being silently skipped. When a folder in your repo is a symlink to a location outside the repo root — the standard layout for Dota 2 custom games and similar SDK-linked projects, where `game/` and `content/` link into the engine tree — CodeGraph followed the symlink to discover those files but then blocked every one of them while reading, logging `Path traversal blocked in batch reader` and indexing nothing under them. The reader now agrees with the directory scan and indexes those files. The guard against `../` path escapes is unchanged, and the protection that keeps your agent from being served file contents from outside the repo is also unchanged — only the indexer's own read path follows these in-repo symlinks. (#935)
 
 
 ## [1.0.1] - 2026-06-13