fix(mcp): honor workspace filters and shared engine resource controls

[Christopher-Schulze]

Fixes #23.

Generated source files in an ignored directory currently enter the graph through MCP file events, even when initial indexing excludes them. Each batch then repeats full-graph path queries for individual files. This change gives workspace indexing and the MCP watcher the same filters and makes the existing shared-engine mode preserve the resource settings needed for parallel agent sessions.

Changes

• Share compiled exclusions and cached root/nested .gitignore matchers between directory indexing and watcher filtering. Preserve .codegraphignore, CLI excludes and built-in exclusions; apply size/depth limits and enforce the file limit for new watcher entries. Reload ignore rules on changes without reacting to read-access notifications.
• Group graph nodes by path once per watcher batch instead of repeating full-graph property queries. Rebuild search indexes after deletion-only batches, prune orphan vectors after node removal, and cancel the watcher task when its owner is dropped.
• Skip memory-manager/model initialization in graph-only indexing, including warm daemon snapshots.
• Forward resource flags during engine auto-start, apply graph-only/profile settings to shared backends, serialize workspace initialization with OnceCell, and hold a per-socket file lock through startup and the engine lifetime.
• Preserve explicitly supplied workspace arguments in the npm relay wrapper and document repository-local ignores and shared-engine configuration.

The ignore crate supplies Git ignore matching; fs2 was already a workspace dependency. No release/version or default transport changes are included.

Validation

macOS arm64, Rust 1.98.0, isolated homes/workspaces/build output, two build jobs:

• cargo test --locked -p codegraph-server -- --test-threads=1: 412 passed, 0 failed. One existing model-dependent test remains ignored by upstream; no tests were disabled or weakened.
• bun mcp-package/test/wrapper-args.test.js: 14 checks passed. The same updated test file against the unchanged upstream wrapper fails the four explicit-workspace cases.
• Real stdio-MCP reproduction against installed 0.20.1 and the patched debug binary: creating 20 Rust files under a directory excluded by .gitignore, .codegraphignore and --exclude produces searchable unwanted symbols before the patch, and none afterward. The original invokes MemoryManager::initialize under --graph-only; the patched binary does not. Both runs use the local static backend with an absent model path to avoid model downloads.
• Regression coverage includes real filesystem events, nested ignore/negation rules, deleted paths, size/depth/file limits, graph-only one-shot execution, concurrent cold workspace attaches and two real auto-starting socket relays.
• cargo clippy --locked -p codegraph-server --all-targets --no-deps completes with existing warnings. -D warnings also fails on unchanged upstream 64f4f30 (unused/dead code and existing Clippy findings); the patch adds no diagnostic at a changed/new source location. A global RUSTFLAGS=-Dwarnings build likewise stops at the pre-existing BODY_PREFIX_MAX_CHARS import in codegraph-c/src/visitor.rs.
• Scoped rustfmt checks and git diff --check pass. Full-workspace cargo fmt --all -- --check already reports unrelated upstream formatting differences; those files are untouched.

Behavior boundaries

Engine options remain process-wide: the first starter configures a socket; later clients do not reconfigure it. The README documents consistent settings, explicitly managed engines, separate sockets and restarting after configuration changes. Existing indexed entries require a forced reindex after ignore-rule changes. Global Git ignores and .git/info/exclude are outside this change. Direct manual file indexing remains available.

The saved production sample identifies the watcher/query hot path, but does not prove an infinite loop or database corruption. This PR makes no throughput or memory-reduction claim based on the synthetic reproduction.