Add HUMAnN 4 database generation protocols

[lwaldron]

Drafts the 5 ai-agent-compatible protocols required to generate HUMAnN 4 databases.

[Copilot]

Pull request overview

Adds a set of draft, AI-agent-compatible protocols documenting the end-to-end workflow for generating HUMAnN 4 databases (SGB aggregation → augmented clustering → ChocoPhlAn build → translated search build → utility mapping).

Changes:

• Adds a protocol for aggregating and subsampling MetaPhlAn 4.2 SGB genomes/MAGs.
• Adds a protocol for augmented UniRef-compatible ORF clustering and ORF→cluster mapping generation.
• Adds protocols for building ChocoPhlAn nucleotide pangenomes, a DIAMOND translated-search database, and functional utility mapping TSVs.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
protocols/humann4-sgb-aggregation/protocol.md	Defines the SGB genome retrieval and subsampling step that seeds the HUMAnN 4 DB build pipeline.
protocols/humann4-augmented-clustering/protocol.md	Documents ORF prediction, UniRef alignment, de novo clustering, and ORF mapping generation for novel clusters.
protocols/humann4-chocophlan-build/protocol.md	Describes constructing per-SGB nucleotide pangenomes and Bowtie2 indexes for ChocoPhlAn.
protocols/humann4-translated-search-build/protocol.md	Documents building the merged UniRef90 + novel-cluster protein database and DIAMOND index.
protocols/humann4-utility-mapping/protocol.md	Describes generating HUMAnN mapping TSVs by combining UniProt cross-references and eggNOG-mapper outputs.

Suppressed comments (4)

protocols/humann4-utility-mapping/protocol.md:32

• Remove trailing whitespace from the Markdown heading to avoid markdownlint/formatting noise.

## Materials 

protocols/humann4-translated-search-build/protocol.md:32

• Remove trailing whitespace from the Markdown heading to avoid markdownlint/formatting noise.

## Materials 

protocols/humann4-chocophlan-build/protocol.md:32

• Remove trailing whitespace from the Markdown heading to avoid markdownlint/formatting noise.

## Materials 

protocols/humann4-augmented-clustering/protocol.md:32

• Remove trailing whitespace from the Markdown heading to avoid markdownlint/formatting noise.

## Materials 

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