Custom template per chain

It currently seems like the input custom template path is applied for every chain in the input.

https://github.com/sokrypton/ColabFold/blob/main/colabfold/batch.py#L768

        if custom_template_path is not None:
            template_paths = {}
            for index in range(0, len(query_seqs_unique)):
                template_paths[index] = custom_template_path

Which means it is currently impossible to provide a set of templates for each chain. This differs from the mmseq2 server setup, which will generate a indexed set of template paths for each chain:

        a3m_lines_mmseqs2, template_paths = run_mmseqs2(
            query_seqs_unique,
            str(result_dir.joinpath(jobname)),
            use_env,
            use_templates=True,
            host_url=host_url,
        ) 
# template_paths will be a list of length len(query_seqs_unique)

So, there's a lack of feature parity between Colab's implementation of templates and a custom template. I'd be happy to contribute a fix for this, but there's an implementation discussion to be had as to how to extend custom_template_path to be a list + amenable to multimers.

Start in colabfold/batch.py around line 768 and compare the custom-template handling with the run_mmseqs2 call shown in the issue. Clarify the accepted custom_template_path shape and its behavior for multimers, then implement feature parity so each chain can receive its intended templates.