Convert --skip-if-downloaded-already to single flag format

[Copilot]

Per review feedback, simplified the dual flag --skip-if-downloaded-already/--no-skip-if-downloaded-already to a single boolean flag --skip-if-downloaded-already.

Changes

• CLI flags: Converted dual flag to single flag format across all 4 download commands
• Default behavior: Changed from skip-by-default (default=True) to download-by-default (default=False)
  • Without flag: files are re-downloaded even if they exist
  • With flag: existing files are skipped
• Documentation: Updated README and docstrings to reflect new semantics

Example

# Before: Files skipped by default, use --no-skip-if-downloaded-already to force re-download
pridepy download-all-public-raw-files -a PXD001234 -o ./output

# After: Files re-downloaded by default, use flag to skip existing files
pridepy download-all-public-raw-files -a PXD001234 -o ./output --skip-if-downloaded-already

This makes the flag opt-in rather than opt-out, providing more explicit control over download behavior.

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[ypriverol]

@copilot --skip-if-downloaded-already must be a flag.

[Copilot]

@copilot --skip-if-downloaded-already must be a flag.

The --skip-if-downloaded-already is already implemented as a flag with is_flag=True. Could you clarify what needs to be changed?

Current implementation:

@click.option(
    "--skip-if-downloaded-already",
    is_flag=True,
    default=False,
    help="Skip the download if the file has already been downloaded.",
)

CLI output shows it as a boolean flag:

--skip-if-downloaded-already    Skip the download if the file has already
                                been downloaded.

Are you concerned about the default behavior (currently False, meaning files are re-downloaded by default unless the flag is present)?