fix: namespace temp directories by username to avoid multi-user conflicts

[Alm0stSurely]

Problem

As reported in #150, OpenFold3 uses hardcoded paths under /tmp/ for temporary directories. On multi-user machines, this causes PermissionError when user A creates a directory (e.g., /tmp/of3_colabfold_msas/) and user B tries to write to it.

Affected paths:

Default path	Location
/tmp/of3_colabfold_msas/	openfold3/core/data/tools/colabfold_msa_server.py:1000
/tmp/of3_template_data/	openfold3/core/data/pipelines/preprocessing/template.py:1605
/tmp/ramdisk/	openfold3/core/data/tools/jackhmmer.py:206

Analysis

The issue occurs because:

1. Directories are created with default permissions (755)
2. The paths are identical for all users on the same machine
3. When user A creates the directory first, user B gets a permission denied error

Solution

Namespace the temporary directories by username, following the pattern used by pytest (/tmp/pytest-of-{user}/):

/tmp/of3-{username}/colabfold_msas/
/tmp/of3-{username}/template_data/
/tmp/of3-{username}/ramdisk/

This ensures each user gets their own isolated directory hierarchy, preventing permission conflicts while maintaining backward compatibility (users can still override via configuration).

Changes

• colabfold_msa_server.py: Added getpass import, namespaced the default MSA output directory
• template.py: Added getpass import, namespaced the default template data directory
• jackhmmer.py: Added getpass and tempfile imports, namespaced the ramdisk directory with automatic directory creation

Testing

• Verified syntax with python3 -m py_compile on all modified files
• Tested path generation logic confirms proper user isolation
• Confirmed no hardcoded /tmp paths remain in the modified files

Notes

• This fix is minimal and non-breaking — users who explicitly set output directories are unaffected
• The pattern mirrors pytest's proven approach for temp directory isolation
• Fixes [BUG] Multi-user machine /tmp/of3-directories cause errors #150

[jandom]

Thank you for this contribution, we've combined it with #151 and both are superseded by #158