Preserve completed component progress when an ingestion task resumes from a checkpoint. Checkpointed operators are skipped and do not emit lifecycle events again, which previously caused the document progress to
remain below 100%.
Fixes the defect where selecting many files (e.g. 20+) in one dataset and starting parsing at once leaves most of them stuck in `RUNNING` forever: a few parse, the rest never do.
### Summary
1. Remove dead code (replaced by builtin ingestion pipeline)
2. Refactor (move document parsing progress from http api into ingestion
executor)
