Merge main into feature/peptdeep-kontext#824
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--- # Conversation that produced these changes --- ## User prompt "Please clone github.com/MannLabs/alphadia, install it into a new conda environment and run the basic e2e test. Along the way, take notes to a markdown file: unclarities errors you ran into things you miss in the documentation The goal is to get input on how to reduce friction in the initial setup of alphadia." Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
remove unused fragments from input during multiplexing
add support for .mzML file selection in InputFileSelect component
Reduce agent friction
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Keep the peptdeep-kontext feature branch in sync with main. Merge is conflict-free.
To-do list (outside contributers only)