redesign calibrate task window to mimic search task window

[trishorts]

This pull request refactors and reorganizes the CalibrateTaskWindow.xaml UI to improve the layout and clarity of the search parameters section. The changes focus on restructuring controls into a more logical grid, enhancing tooltips, and removing redundant or misplaced UI elements. This PR is a prelude to future PRs that will enable calibration with the modern search engine and eventually non-specific peptides.

UI layout improvements and reorganization:

• Replaced nested Expander and StackPanel structures with a grid-based layout for search parameters, resulting in a cleaner and more organized interface.
• Grouped related controls (e.g., protease selection, mass tolerances, missed cleavages, modifications, peptide lengths, dissociation type, and separation type) into specific grid rows and columns for better usability and logical flow. [1] [2] [3] [4]

Removal and relocation of parameters:

• Removed the "File Loading Parameters" section and several less frequently used or advanced options (such as max modification isoforms, max threads, and variant-related controls) from the main search parameters area to streamline the user experience. [1] [2] [3] [4]

Tooltip and labeling enhancements:

• Improved tooltips and labels for several controls to provide clearer guidance to users, including more descriptive explanations for protease selection, modification limits, and separation type. [1] [2] [3]

Addition of new or reorganized controls:

• Added or repositioned controls for "Dissociation Type" and "Separation Type" to make them more prominent and accessible within the search parameters grid. [1] [2]

[Copilot]

Pull request overview

This PR restructures the Calibrate Task window UI to align more closely with the Search Task window, improving organization of search-related controls and moving seldom-changed parameters into an “Advanced Options” section.

Changes:

• Replaced the previous nested Expander/StackPanel structure for core search parameters with a 2-column grid grouping protease, mass tolerances, missed cleavages, peptide length, dissociation type, and separation type.
• Moved file loading parameters, max modification isoforms, variant-related settings, max threads, and minimum score into an Advanced Options expander, grouped into dedicated sub-sections.
• Updated several labels and tooltips for clarity and consistency (e.g., more descriptive explanations for protease, modification limits, and separation type).

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.72%. Comparing base (4a3ab6f) to head (d1075ef).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2612   +/-   ##
=======================================
  Coverage   94.72%   94.72%           
=======================================
  Files         187      187           
  Lines       19658    19658           
  Branches     3636     3636           
=======================================
  Hits        18621    18621           
  Misses        566      566           
  Partials      471      471           

Flag	Coverage Δ
unittests	94.72% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.