[REF] Refactor phenotypic/BIDS subjects check and add more intermediate stdout for bagel bids

[alyssadai]

Closes #190

Changes proposed in this pull request:

• Check for BIDS subject IDs missing from the phenotypic JSONLD before slow BIDSLayout initialization
  • This is done by simply extracting BIDS subdirectory names (see Check that all BIDS subjects are in pheno.jsonld prior to BIDS parsing #190 issue description for why pybids functions are limited here)
• Print more intermediate messages during bagel bids command to indicate program progress

Checklist

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see https://neurobagel.org/contributing/pull_requests for more info)
• 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.

[github-actions]

Pull Request Test Coverage Report for Build 6601724770

• 30 of 30 (100.0%) changed or added relevant lines in 3 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage increased (+0.006%) to 99.685%

---

Totals
Change from base Build 6579716968:	0.006%
Covered Lines:	1267
Relevant Lines:	1271

---

💛 - Coveralls

[rmanaem]

🧑‍🍳