Add input/output descriptions to --help for 95 CLI scripts

[olsonanl]

Summary

• Adds Input/Output/Example lines to --help output for 95 p3- scripts
• Clarifies for each script whether it reads from stdin, command-line arguments, files, or a combination
• Covers all three input patterns:
  • CLI-only queries: p3-all-*, p3-find-serology-data, etc. — "Input: none (queries BV-BRC database directly)"
  • Stdin pipeline: p3-get-*, p3-find-features, data utilities — "Input: tab-delimited genome IDs on stdin (or --input file)"
  • Dual-mode: p3-gto, p3-dump-genomes — "Input: genome IDs as arguments, or - to read from stdin"

Depends on P3Utils::input_spec() from p3_core PR: BV-BRC/p3_core#20

Motivation

Users frequently struggle with understanding which scripts read from stdin vs command-line arguments, and how to compose them into pipelines. This adds the answer directly to --help where they look first.

Example

$ p3-get-genome-features --help

  Input:   tab-delimited genome IDs on stdin (or --input file)
  Output:  tab-delimited feature data
  Example: p3-all-genomes --eq genus,Methylobacillus | p3-get-genome-features --attr patric_id --attr product

p3-get-genome-features.pl [-abcefhiKr] [long options...]
  ...

Scripts not modified (3)

p3-aggregates-to-html, p3-project-subsystems, p3-make-genome-list-blast-database — these don't use P3Utils::script_opts() and need individual handling.

Test plan

• Spot-checked --help output for scripts from each category
• All 95 modified scripts produce valid help output
• Unmodified scripts still work unchanged

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