Fix module/cluster prompts exceeding codex input cap; fix resume skipping missing module docs

[anhnh2002]

Problem

Two independent failures observed while generating docs for wazuh (822 modules, 20.8k components):

1. input_too_large on module generation. format_user_prompt inlines the entire module tree — every component of every module — into each module agent's prompt. On wazuh the tree alone formats to ~823k chars; together with an inlined 350k-char source file the prompt reached 1,175,972 chars, over codex's hard per-turn input cap of 1,048,576 chars (input_too_large, code -32602). Every remaining module failed deterministically. Same bug family as the overview prompts fixed in Fix overview generation failing on large repos (codex input_too_large) #92, in a different code path. format_cluster_prompt has the same exposure.

2. Resume silently skipped missing docs. run_module_agent (caw and pydantic-ai backends) and generate_parent_module_docs returned early whenever overview.md existed. overview.md only proves the root module is done, so resuming a partial run skipped every nested module and parent that still lacked its own doc file.

Fix

• prompt_template.py: build the prompt with the full tree exactly as before; only if it exceeds MAX_USER_PROMPT_CHARS (900k, leaving headroom for system prompt and protocol overhead), rebuild with a names-only tree (~26k chars for wazuh) plus a note pointing the agent at its reading tools. As a last resort, truncate inlined file contents (recoverable — the agent has read_code_components / str_replace_editor). Same guard on format_cluster_prompt. The duplicated tree-formatting closures are extracted into _format_module_tree_str. Prompts under the cap are byte-identical to before (verified against ml-agents, electron, and wazuh module trees).
• Backends: gate the overview.md early-return on the root module (empty module_path) so every other module is checked against its own doc file.
• Mechanical ruff cleanup on the touched backend files so the changed-files lint job passes.