fix: add retry logic and checkpoint support for filter command

[mosumosu-JAPAN]

fix: retry logic and checkpoint support for filter command

[mosumosu-JAPAN]

What this fixes

Two bugs that cause kompile filter to crash on large datasets:

1. Retry logic: Haiku occasionally returns a list instead of a dict,
   or invalid JSON. Added up to 3 retries before discarding the source.

2. Checkpoint support: Filter now saves progress after each source,
   So a crashed run resumes from where it left off instead of restarting
   from the beginning.

Tested on around 1500～ Claude conversations.