DOCS-2791 Fix dxda help strings

[dx-janc]

Summary

Fix the Download Agent CLI help output so the generated help strings are clearer and match the actual command behavior.

This keeps the scope limited to help text and help rendering. It does not add tests or change command behavior.

What changed

• Replaced the generic top-level help output with a Download Agent-specific overview.
• Updated the top-level description to reference the DNAnexus Platform.
• Fixed the inspect -h usage line so it no longer shows the download usage.
• Replaced the old inspect synopsis with clearer integrity-validation wording.
• Updated the inspect flag description to say validating files instead of downloading files.
• Improved subcommand help formatting so the usage line, synopsis, and flags are separated cleanly.
• Added clearer synopsis output for commands -h, flags -h, progress -h, and version -h.

Before and after examples

dx-download-agent -h

Before:

Usage: dx-download-agent-old <flags> <subcommand> <subcommand args>

Subcommands:
        commands         list all command names
        download         Download files in a manifest
        flags            describe all known top-level flags
        help             describe subcommands and their syntax
        inspect          Inspect files downloaded in a manifest + additional 'health' checks
        progress         show current download progress
        version          get the version

After:

dx-download-agent v0.6.3
CLI tool to manage the download of files from the DNAnexus Platform

Usage:
  dx-download-agent download [-num_threads=N] <manifest.json.bz2>
  dx-download-agent inspect [-num_threads=N] <manifest.json.bz2>
  dx-download-agent progress <manifest.json.bz2>
  dx-download-agent version

Authentication:
  Set DX_API_TOKEN or configure ~/.dnanexus_config/environment.json.

Primary commands:
  download        Download files in a manifest
  inspect         Inspect files downloaded in a manifest and validate their integrity
  progress        Show current download progress

Reference commands:
  version         Get the version
  help            describe subcommands and their syntax
  flags           describe all known top-level flags
  commands        list all command names

dx-download-agent commands -h

Before:

commands:
        Print a list of all commands.

After:

commands:
        Print a list of all commands.

list all command names

dx-download-agent flags -h

Before:

flags [<subcommand>]:
        With an argument, print all flags of <subcommand>. Else,
        print a description of all known top-level flags.  (The basic
        help information only discusses the most generally important
        top-level flags.)

After:

flags [<subcommand>]:
        With an argument, print all flags of <subcommand>. Else,
        print a description of all known top-level flags.  (The basic
        help information only discusses the most generally important
        top-level flags.)

describe all known top-level flags

dx-download-agent download -h

Before:

dx-download-agent download [-num_threads=N] <manifest.json.bz2>  -gc_info
        report statistics for golang garbage collection
  -max_threads int
        An alias for num_threads
  -num_threads int
        Number of threads to use when downloading files. By default (or if zero), this number is chosen according to machine memory and CPU constraints.
  -verbose
        verbose logging

After:

dx-download-agent download [-num_threads=N] <manifest.json.bz2>

Download files in a manifest

  -gc_info
      report statistics for golang garbage collection
  -max_threads int
      An alias for num_threads
  -num_threads int
      Number of threads to use when downloading files. By default (or if zero), this number is chosen according to machine memory and CPU constraints.
  -verbose
      verbose logging

dx-download-agent inspect -h

Before:

dx-download-agent download [-num_threads=N] <manifest.json.bz2>  -num_threads int
        Number of threads to use when downloading files. By default (or if zero), this number is chosen according to machine memory and CPU constraints.
  -verbose
        verbose logging

After:

dx-download-agent inspect [-num_threads=N] <manifest.json.bz2>

Inspect files downloaded in a manifest and validate their integrity

  -num_threads int
      Number of threads to use when validating files. By default (or if zero), this number is chosen according to machine memory and CPU constraints.
  -verbose
      verbose logging

dx-download-agent progress -h

Before:

dx-download-agent progress <manifest.json.bz2>

After:

dx-download-agent progress <manifest.json.bz2>

Show current download progress

dx-download-agent version -h

Before:

get the dx-download-agent version

After:

dx-download-agent version

Get the version

Validation

• Built the current branch and upstream master binaries locally and compared the main help-producing commands side by side.
• Ran go test ./... in an isolated HOME/PATH environment to avoid local DNAnexus config leaking into existing tests.