gfa2vcf output is always stdout

[urbanslug]

Problem Description

When running povu gfa2vcf, the output VCF is always directed to stdout, even when the user specifies the --output-dir option.
The CLI help text leads users to believe they can output VCF files to a directory.

Expected Behaviour

When the user specifies the --output-dir option, the VCF output should be written as separate files in the specified directory.

Actual Behavior

Regardless of whether --output-dir is provided or not, the VCF output is always sent to stdout.
This is because of this https://github.com/pangenome/povu/blob/main/app/subcommand/gfa2vcf.cpp#L64

Suggested Solution

Make stdout the default output stream for VCF output (as it currently is), but fix the --output-dir option so that when the user sets --output-dir, the VCF should be written as files in the given directory.

This ensures the CLI options are mutually exclusive and their descriptions are consistent with the actual behavior.

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Additional Context

$ povu gfa2vcf -h
Flag '--input-gfa' is required
  povu gfa2vcf {OPTIONS} [refs...]

    Convert GFA to VCF (decompose + call)

  OPTIONS:

      -i[gfa], --input-gfa=[gfa]        path to input gfa [required]
      Decompose options
        -h, --hairpins                    Find hairpins in the variation graph
                                          [default: false]
        -s, --subflubbles                 Find subflubbles in the variation
                                          graph [default: false]
      Streaming options
        -c[chunk_size],
        --chunk-size=[chunk_size]         Number of variants to process in each
                                          chunk [default: 100]
        -q[queue_length],
        --queue-length=[queue_length]     Number of chunks to buffer [default:
                                          4]
      Output destination (choose
      exactly one)
        -o[output_dir],
        --output-dir=[output_dir]         Output directory [default: .]
        --stdout                          Output single VCF to stdout instead of
                                          separate files [default: false]
      Reference source (choose exactly
      one)
        -r[prefix_list],
        --prefix-list=[prefix_list]       path to file containing reference name
                                          prefixes [optional]
        -P[path_prefix...],
        --path-prefix=[path_prefix...]    All paths beginning with NAME used as
                                          reference (multiple allowed)
                                          [optional]
        refs...                           list of refs to use as reference
                                          haplotypes [optional]
      "--" can be used to terminate flag options and force all following
      arguments to be treated as positional options