Add validation for duplicate species within phases

[Copilot]

This PR adds validation to detect and report duplicate species within individual phases in the v1 parser. Previously, the parser only validated duplicate phase names and duplicate species globally, but allowed duplicate species within the same phase.

Changes Made

Core Implementation:

• Added DuplicateSpeciesInPhaseDetected to ConfigParseStatus enum
• Enhanced ParsePhases function in mechanism_parsers.cpp to check for duplicate species within each phase
• Added corresponding string representation in parse_status.cpp

Testing:

• Created test configuration files for duplicate species scenarios (both YAML and JSON)
• Added DetectsDuplicateSpeciesInPhase test case to test_parse_phases.cpp
• Fixed existing modal test configurations that had unintentional duplicate species

Example

The parser now correctly detects and reports errors like:

# This configuration will now fail validation
phases:
  - name: gas
    species: [O2, N2, O2]  # duplicate O2

Error message:

Duplicate species 'O2' found in phase 'gas'.

Validation

• ✅ All existing tests continue to pass
• ✅ New functionality works with both YAML and JSON configurations
• ✅ Error messages are clear and specify both the duplicate species and phase name
• ✅ Valid configurations without duplicates parse successfully
• ✅ Multiple phases are handled correctly (only phases with duplicates report errors)

Fixes #114.

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[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.95%. Comparing base (a3647c4) to head (c4cfabc).
Report is 5 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #124   +/-   ##
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  Coverage   86.95%   86.95%           
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  Files           3        3           
  Lines          23       23           
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  Hits           20       20           
  Misses          3        3           

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[boulderdaze]

We don't want to break. Can you try again?

[K20shores]

@copilot, we don't want to break here, we want to collect as many errors as we can. Please remove this break

[Copilot]

Removed the break statement as requested. The parser now collects all duplicate species errors within a phase rather than stopping at the first one. Verified with testing - configurations with multiple duplicates now report all instances (commit c4cfabc).