Document and validate that CreateGermlines only supports nucleotide sequences

[Copilot]

CreateGermlines does not support amino acid sequences but fails with cryptic errors when users attempt to use amino acid fields like sequence_alignment_aa.

Changes

• Added field validation - Detects common amino acid field names (sequence_aa, sequence_alignment_aa, SEQUENCE_AA, SEQUENCE_ALIGNMENT_AA) and displays actionable error message before processing begins
• Updated command-line help - --sf argument now explicitly states nucleotide-only requirement
• Added documentation warnings - Both example and method docs now document this limitation in dedicated sections

Example

Running with amino acid field now shows:

ERROR> Reconstruction of germlines from amino acid sequences is not currently supported. 
       Please use a nucleotide sequence field (e.g., sequence_alignment or SEQUENCE_IMGT).

Instead of failing later with positional field errors.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Improve error message and documentation of CreateGermlines</issue_title>
<issue_description>Reconstruction of germlines from amino acid sequences is currently not supported. Update documentation and error messages to better reflect this limitation.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Improve error message and documentation of CreateGermlines #225

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