Add validation error for incompatible transcript_fasta and additional_fasta params

[Copilot]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
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• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

When --transcript_fasta and --additional_fasta are both provided without a pre-built pseudo-aligner index, the pipeline fails at quantification with a cryptic "missing transcripts" error. This happens because:

• additional_fasta sequences are appended to the genome FASTA/GTF
• But user-provided transcript_fasta is used as-is (without spike-ins) for building the index

Changes

• Validation: Fail fast with clear error when building a pseudo-aligner index from transcript_fasta while additional_fasta is also set
• Index-specific check: Only validates the relevant index for the selected pseudo-aligner (salmon_index for salmon, kallisto_index for kallisto)
• Test fix: Kallisto test now sets additional_fasta = null since no kallisto index with spike-ins exists in test datasets
• Documentation: Updated schema help text and usage docs with compatibility notes

Valid configurations

The combination is allowed when a pre-built index containing the spike-ins is provided:

# This will error (index built without spike-ins)
--transcript_fasta tx.fa --additional_fasta ercc.fa --pseudo_aligner salmon

# This works (pre-built index already has spike-ins)
--transcript_fasta tx.fa --additional_fasta ercc.fa --salmon_index /path/to/index

Closes #1450

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