Add Peptidoform Scoring Control

[yueqixuan]

Testing completed: (Phase 2) 2d. Phospho: Peptidoform Scoring Control

DIA-NN: (--no-peptidoforms) disables automatic activation of peptidoform scoring when variable modifications are declared, not recommended.

After testing, the DIA-NN log only stops showing "WARNING: peptidoform scoring enabled because variable modifications have been declared; to disable, use --no-peptidoforms : 1" when diann_no_peptidoforms is applied in all subworkflows.

Subworkflows
INSILICO_LIBRARY_GENERATION
PRELIMINARY_ANALYSIS
ASSEMBLE_EMPIRICAL_LIBRARY
INDIVIDUAL_ANALYSIS
FINAL_QUANTIFICATION

New params:

Parameter	Type	Default
--diann_no_peptidoforms	boolean	false

Tested (Run PXD026600 with --diann_no_peptidoforms true):

Version	Test Passed
2.0	✅
2.1.0	✅
2.2.0	✅
2.3.2	✅

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