chore: remove zero-byte stub modules with no references (duplicated inline in rag/engine.py)

[man4ish]

What

Removes 9 zero-byte stub files (0 bytes each, no content, never implemented):

• retrieval/reranker.py
• retrieval/context_builder.py
• ingestion/plugin_loader.py
• ingestion/repo_fetcher.py
• processing/graph_builder.py
• processing/metadata_builder.py
• index/keyword_index.py
• utils/__init__.py — this was the only file in utils/, so the whole directory is removed
• scripts/ingest.py

Reference search (before deleting)

Searched the full codebase — .py, .md, .yaml/.yml, .toml, .cfg, .txt, .sh — for each module by dotted path (e.g. retrieval.reranker) and by bare name (e.g. reranker), plus a repo-wide sweep for importlib, ImportError (try/except fallback-import patterns), and any utils package usage.

Result: zero functional references to any of the 9 modules anywhere outside their own file. No imports, no __init__.py re-exports, no dynamic importlib loading, no try/except ImportError fallbacks.

One non-functional hit found, as required to report: README.md:132 lists scripts/ingest.py in the "Repository Structure" file tree (├── ingest.py # Standalone ingestion helper). This is a stale doc comment, not a code dependency — the file itself is empty and does nothing. It was not a blocker for deletion but is worth a follow-up doc cleanup (out of scope for this PR).

The retrieval.rerank() and retrieval/context-building functionality these stubs' names suggest already exists — implemented inline in rag/engine.py (RAGEngine.rerank() at rag/engine.py:143, RAGEngine.build_context() at rag/engine.py:214) — confirming these stub files were leftover dead placeholders, never wired up.

Test suite parity

• Before deletion: pytest -q → 174 passed
• After deletion: pytest -q → 174 passed

Identical pass count, no new failures. Diff is 9 files deleted, all empty (0 insertions / 0 deletions per file since they had no content).

Scope

No code logic touched — every deleted file was 0 bytes.