fix: multi-user machine permission errors on /tmp created dirs

[jandom]

Summary

Fix shared /tmp directories that cause PermissionError on multi-user machines.

Introduces a centralized get_of3_tmpdir() utility that namespaces temp dirs per user, following the same convention as pytest (/tmp/pytest-of-alice/ → /tmp/of3-of-alice/).

Changes

• New get_of3_tmpdir(subdir) in openfold3/core/data/tools/utils.py — single source of truth for OF3 temp directories
• Each user gets /tmp/of3-of-$USERNAME/<subdir>/ — no more cross-user permission conflicts
• Respects $TMPDIR, $TEMP, $TMP and other platform conventions via tempfile.gettempdir()
• Migrated colabfold_msa_server.py, template.py, and jackhmmer.py off hardcoded /tmp paths
• Added 9 tests in test_utils.py covering path structure, isolation, idempotency, and $TMPDIR support

Related Issues

• Fixes [BUG] Multi-user machine /tmp/of3-directories cause errors #150
• Supersedes fix: use user-specific temp directories to avoid permission errors #151 fix: namespace temp directories by username to avoid multi-user conflicts #152

Testing

pytest openfold3/tests/core/data/tools/test_utils.py

Other Notes

[jnwei]

This is good, thank you for updating the tmp directory throughout the repo.

Two comments:

• For the jackhmmer workflow, I am not sure if it is preferable to have the results moved to a user subdirectory. If a user is running a large number of alignments with jackhmmer, chances are that they would want to use the alignments with other users / roles, and may prefer to just change the permissions manually for the directory. @vinay-swamy do you have thoughts about this?

• Could you also update the full configuration reference doc?
  I think it should just be msa_computation_settings

[jandom]

Good shout on the docs – for the jackhammer, it seems to me like it was something super custom to run in a setup where you had /tmp in RAM, so indeed might not be appropriate to store that under. it's also not impacting the original test problem.

[jnwei]

LGTM. I would suggest that we leave the tmp pipeline for jackhmmer alone for now, since that is a fairly different pipeline. We can change the tmp dir later if needed.

[jandom]

Agreed on jackhammer

[vinay-swamy]

tbh I think its better to deprecate the old python based jackhmmer workflow - It would be better to instead point users to the snakemake workflow as that will generally be faster than the previous method

[jandom]

tbh I think its better to deprecate the old python based jackhmmer workflow

let's mark as deprecated for Q2 in another PR, and not mess around with it in this PR – thanks @vinay-swamy