Potential race conditions & incomplete atomic JSON write | proposing fixes

[Lix-fl]

Hello

Thank you for open sourcing this project it looks very promising

While reading through the code I noticed a few issues that could cause instability in concurrent or long running scenarios I wanted to open an issue first before submitting any pull request

Observations

1 atomic_write_json appears to be incomplete
The function creates a temporary path but does not write json data fsync the file or atomically replace the target file This could result in corrupted state or config files if the process stops unexpectedly

2 Possible race conditions in global rate limiting
GLOBAL_RATE_LIMIT_DELAY is modified under a lock but read without a lock This can lead to inconsistent behavior when multiple jobs run at the same time

3 Pipeline step mismatch
The PIPELINE_STEPS list includes screenshots but this step is not defined as a tool or gate This may cause unexpected behavior or runtime errors

4 Directory initialization order
Some file operations may happen before ensure_dirs is guaranteed to run which could cause FileNotFoundError in some edge cases

Proposed action

If these changes align with your direction I would be happy to submit a pull request that
Completes atomic_write_json with safe atomic writes
Adds proper locking around global rate limit state
Cleans up pipeline and tool mismatches
Keeps changes minimal and consistent with the current code style

Please let me know if you are open to these improvements

Thanks