[FIX] Do not apply substitutions immediately when loading invocations

[michellewang]

• Closes none

Changes proposed in this pull request:

• This PR reverts a change in [ENH] Make HPC_CONFIG_FILE use a relative path #622 where substitutions were applied to invocations immediately on load. It turns out this causes some problems (and warnings) since invocations require on-the-fly substitutions related to participant/session IDs

Checklist (for reviewers)

This section is for the PR reviewer

• PR has an interpretable title with a prefix (e.g. [BUG], [DOC], [ENH], [MAINT])
  Refer to NumPy Development Guide for a full list
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions

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📚 Documentation preview 📚: https://nipoppy--627.org.readthedocs.build/en/627/

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
nipoppy/workflows/pipeline.py	100.00% <ø> (ø)

... and 3 files with indirect coverage changes

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[mathdugre]

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