Show persistent best practice results in workflow editor

[mvdbeek]

Persistent and Reactive Best Practices in Workflow Editor

This PR significantly improves the Best Practices activity in the workflow editor, making it persistent, reactive, and
more user-friendly. It also adds the ability to refactor specific workflow versions and updates the workflow object on every save (updating step indices to prevent having inconsistent indices).

persistent_best_practice_results_FINAL.mp4

---

Best Practices Activity Improvements

Progress Tracking & Visual Feedback

• Progress indicators show resolved vs total issues on both the activity icon and within the panel
• Separate sections for critical (high priority) issues and attribute-based recommendations
• 🎉 Success reaction when all best practices are met

Progress Indication/Separate Sections	Celebratory Reaction when done🎉

Loading overlay during workflow save operations

New Workflow Editor Loading Overlay

Interactive Highlighting

• Hover highlighting on lint items highlights the corresponding step/input/output on the workflow graph
• Duplicate output labels detection added as a new lint check

---

Workflow Version Selector Improvements

• New multiselect component replaces the old version dropdown with better UX
• "Switch to latest version" link appears when editing an older version
• "(latest version)" indicator when on the current version

---

Refactoring Specific Workflow Versions

A new feature allowing users to refactor a specific workflow version (not just the latest):

• Added optional version parameter to the refactor workflow API endpoint
• Confirmation dialog prompts users when attempting to refactor a non-latest version
• The refactored version becomes the new latest version

persistent_best_practice_results_Refactor_old_v.mp4

---

Viewport Transform Retention

Fixes the issue where the viewport would jump after saving or refactoring:

• Transform adjustment compensates for coordinate shifts computed by the backend during normalization
• Extracted to useWorkflowBoundingBox composable with comprehensive tests

---

Bug Fixes & Polish

• Refactored inputs no longer overlap - new inputs created during refactors are positioned to avoid existing steps
• Active step form reopens after save - if editing a step when saving, that step's form reopens after the save
  completes (since now we _loadCurrent on every save)
• Step indices stay consistent - saves now properly update step indices to match backend state
• Converted Lint.vue, LintSection.vue, and RefactorConfirmationModal.vue to Composition API + TypeScript

---

Initial description by Marius

People just keep on creating workflows with disconnected inputs, I really want this to be front and center.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:

1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[mvdbeek]

Just noticed that disconnected when inputs don't appear ... they definitely should though.

[ahmedhamidawan]

I've made minor additions here, and provided a screencast at the top. Will provide a detailed description once all is complete.

For now, there are a few remaining items/bugs I am working on:

• The hover highlighting on inputs/outputs/entire steps can also be inaccurate when there are changes made and saved (seems like a store update is needed for positioning)
• Jests need to be fixed/updated ✅ Fixed! I've added extensive vitests for best practices that should be sufficient
• Now every save in the editor resets the entire editor positioning. Make that smoother ✅ Fixed! I've made it so we return to the original bounding box before the save. There is also a nice loading overlay on each save.
• Move the activity higher up
• Collapse completed items
• Adjust the best practices for high and low priorities, and only show high priority counts on the activity
• The auto fixed inputs would appear on top of each other
• Major bug: When you go about refactoring/linting a prior version with a different set of steps etc, it breaks because the backend looks at the latest version of the workflow
• This is unrelated but it would be cool to improve that version dropdown to have the selected version be highlighted more

[ahmedhamidawan]

Failing tests should be unrelated

[davelopez]

Super cool! Thank you all!

[mvdbeek]

Thank you @ahmedhamidawan!