Add DeNovoGUI compatibility APIs to Utilities

[BioGeek]

Purpose

This PR adds a narrow compatibility layer needed by the DeNovoGUI InstaNovo port after moving DeNovoGUI onto the newer Utilities line.

DeNovoGUI still uses several older Utilities API shapes, especially string-based spectrum keys and legacy PSM iteration helpers. This PR restores those compatibility entry points on top of the current Utilities implementation instead of copying local Utilities classes into DeNovoGUI.

Changes

• Adds legacy spectrum-key helpers:
  • Spectrum.getSpectrumKey
  • Spectrum.getSpectrumFile
  • Spectrum.getSpectrumTitle
• Adds PsmIterator as a small facade over the current spectrum-match iterator.
• Adds compatibility methods used by DeNovoGUI result tables, QC plots, and text exports.
• Adds older convenience accessors for peptides, modifications, precursors, annotation settings, search settings, and tool parameters.
• Keeps the implementation as wrappers around current Utilities APIs where possible.

Tests

Ran:

mvn -DskipTests -Dmaven.javadoc.skip=true package

The main downstream verification is compiling and smoke-testing the DeNovoGUI branch against this Utilities branch.

Merge Order

1. Add InstaNovo and InstaNovo+ import support #73
2. Add SearchGUI support for InstaNovo and InstaNovo+ searchgui#387
3. Add PeptideShaker import UI support for InstaNovo result files peptide-shaker#570
4. This PR
5. Add InstaNovo support to DeNovoGUI denovogui#53
6. Update SearchGUI recipe to 4.3.17 bioconda/bioconda-recipes#66604
7. Update PeptideShaker recipe to 3.0.13 bioconda/bioconda-recipes#66603
8. Expose InstaNovo workflows in online input form barsnes-group/peptide-shaker-online#30
9. Bump PeptideShaker wrappers for InstaNovo support galaxyproteomics/tools-galaxyp#828