Handle mikropml assay and altExp outputs

[0xMuluh]

Summary

• handle preprocessing results stored as assays or alternative experiments
• retrieve removed-feature metadata from the correct location
• pass the detected preprocessing location to run_ml()

Validation

• git diff --check
• affected ML chunks parse successfully
• synthetic assay and altExp storage cases pass
• full mikropml workflow unavailable locally because mikropml is not installed

Closes #860