spec generation: LLM drops source extension when writing sidecar files, causing false "missing spec" retries and pipeline exit

[404MaximWang]

Summary

During spec generation, the LLM occasionally writes .spec.json / .info.json sidecar files without the source file extension (e.g. Preprocessor::preprocess_source.spec.json instead of Preprocessor::preprocess_source.rs.spec.json). Because is_file_ready() expects the full filename including extension ({file_path}.spec.json), the pipeline falsely concludes these functions have no specs, retries 5 times, and then exits with an error. The repeated retries also burn significant API quota and memory.

Reproduction

1. Run FM-Agent on a Rust project:

   uv run python main.py /path/to/dsv4-ccc --submodule src/frontend

2. Wait for spec generation on files with :: in the name (e.g. Preprocessor::preprocess_source.rs).

3. Observe that some functions get xxx.spec.json instead of xxx.rs.spec.json.

4. Pipeline retries 5 times, then exits:

   [Pipeline] ERROR: Stage 6 Layer 2 failed after 5 attempts. 
   2 function(s) are still missing valid specs.
   

Root Cause

The batch prompt tells the LLM:

For each function file `<function-file>`, write TWO JSON files in the SAME directory:

`<function-file>.spec.json`:

For Preprocessor::preprocess_source.rs, the LLM interprets <function-file> as the basename without extension, producing Preprocessor::preprocess_source.spec.json instead of Preprocessor::preprocess_source.rs.spec.json.

This is inconsistent — for some functions the LLM writes the correct name (ExprId::of.rs.spec.json), for others it drops .rs.