chore: update deps, silence warnings, and improve caching/locking

- Cargo.lock: add/adjust packages (atty, dirs 5.0.1, dotenv, hermit-abi 0.1.19, redox_users 0.4.6) and add older windows-targets/windows_* entries; bump windows-sys usages to 0.61.1 where needed.
- crates/codegraph-mcp: add workspace deps (once_cell, lru, atty) in Cargo.toml; integrate indicatif MultiProgress into indexer CLI and switch tracing to a fmt layer.
- FAISS/Vector caching: use once_cell::sync::Lazy statics, store IndexImpl behind parking_lot::Mutex/Arc in INDEX_CACHE, update get_cached_index signature and lock before search; convert EMBEDDING_GENERATOR and QUERY_RESULT_CACHE to Lazy.
- Lint/cleanup: add #![allow(dead_code, unused_variables, unused_imports,...)] to many modules; prefix unused locals with _ to suppress warnings; remove unused imports and simplify imports across multiple files.
- Various small refactors/bugfixes:
  - Use write lock / as_mut when FAISS API requires mutable access.
  - Pass file collection config through indexer flow and fix parser borrow.
  - Minor type/import adjustments in parser, graph, and vector crates to reduce unused symbols and tighten signatures.
  - Small safety/clarity tweaks in onnx, context retriever, search, and insights generator modules.

These changes are primarily maintenance: keep the workspace compiling cleanly, reduce warnings, and improve concurrent caching for vector indexes.

Author: jruokola

Cargo.lock

@@ -40,16 +40,16 @@ open ~/Downloads/LMStudio-*.dmg
 1. Open LM Studio
 2. Go to "Discover" tab
 3. Search and download:
-   - **Embeddings**: `jinaai/jina-embeddings-v3` (1.5B parameters, 1536-dim)
+   - **Embeddings**: `jinaai/jina-code-embeddings-1.5b` (1.5B parameters, 1536-dim)
    - **LLM**: `lmstudio-community/DeepSeek-Coder-V2-Lite-Instruct-GGUF`
      - Select: `DeepSeek-Coder-V2-Lite-Instruct-Q4_K_M.gguf`
 
 **Option B: Manual Download**
 
 ```bash
 # Download embeddings model
-huggingface-cli download jinaai/jina-embeddings-v3 \
-  --local-dir ~/.cache/lm-studio/models/jinaai/jina-embeddings-v3
+huggingface-cli download jinaai/jina-code-embeddings-1.5b' \
+  --local-dir ~/.cache/lm-studio/models/jinaai/jina-code-embeddings-1.5b'
 
 # Download LLM model
 huggingface-cli download lmstudio-community/DeepSeek-Coder-V2-Lite-Instruct-GGUF \
@@ -108,7 +108,7 @@ Create `.codegraph.toml`:
 ```toml
 [embedding]
 provider = "lmstudio"
-model = "jinaai/jina-embeddings-v3"
+model = "jinaai/jina-code-embeddings-1.5b"
 lmstudio_url = "http://localhost:1234"
 dimension = 1536
 batch_size = 64