Fix overview generation failing on large repos (codex input_too_large)

[anhnh2002]

Problem

On large repos, every parent/repo overview call fails. The overview prompt embeds the entire module tree (every module's components list, json.dumps(indent=4)) plus the full markdown of every child doc. On wazuh that is ~2.2M chars — over codex's hard per-turn input cap of 1,048,576 chars. codex rejects the turn instantly (input_too_large, code -32602), and the failure surfaced misleadingly as LLM returned empty content ... (possible output truncation at max_tokens) — 84 consecutive overview failures in a single wazuh run.

Fix

• build_overview_structure strips components lists recursively and replaces inlined child docs with an absolute docs_path per child (None when the doc file is missing). Measured on wazuh: overview prompts drop from ~2.2M to ~83K chars.
• REPO_OVERVIEW_PROMPT / MODULE_OVERVIEW_PROMPT now instruct the agent to read the referenced doc files itself. backend.complete() runs with ToolGroup.READER (codex: --sandbox read-only), so file reads are available. Format placeholders are unchanged, so the MCP prompt_server rendering path keeps working.
• coding-agent-wrapper is pinned to a fork branch (https://github.com/anhnh2002/caw/tree/fix/codex-exec-robustness) carrying the matching codex provider fixes: prompt via stdin (argv size limits), codex exec resume sandbox flag mapping, and no longer silently returning an empty turn when the codex CLI exits nonzero after printing a plain-text Error: line.
• Second commit is mechanical lint cleanup of the touched files (the Lint job runs ruff over whole changed files, including pre-existing violations); it also removes two duplicated dict keys in EXTENSION_TO_LANGUAGE.

Tests

• New tests/test_overview_structure.py: components stripped at every depth, docs referenced by absolute path and not inlined, target marking, and a wazuh-scale synthetic tree staying an order of magnitude under the codex cap.
• Full suite: 46 passed. ruff check + ruff format --check clean on all changed files.
• Verified live against the failed wazuh run: a previously-failing parent overview now generates correctly (the codex agent reads the child docs from the given paths).