chore: repoint legacy repository URLs (org migration 2026-09-22)

[ActInfInstitute]

Summary

Repoints legacy repository URLs after the org/repo migration (Journal-Utilities → Journal_Utilities). Old URLs redirect, but checked-out files should reference canonical names.

Per-file replacements (11 URLs total):

• AGENTS.md (1): generator link (line 18)
• CONTRIBUTING.md (1): repo link (line 13)
• README.md (2): tooling link (11), "Learn more" repo link (54)
• SECURITY.md (1): repo link (22)
• data/AGENTS.md (1): repo link (4)
• data/video/activeinferenceinstitute/AGENTS.md (1): repo link (7)
• docs/AGENTS.md (1): repo link (9)
• docs/PIPELINE.md (1): engine link (4)
• docs/README.md (2): PIPELINE.md table link (13), repo link (26)

⚠️ Requires a token with workflow scope — NOT included in this PR

Two GitHub Actions checkout URLs also need repointing but the PAT used for this PR lacks workflow scope (push of workflow files was rejected by GitHub):

• .github/workflows/deploy-pages.yml line 31: repository: ActiveInferenceInstitute/Journal-Utilities → ActiveInferenceInstitute/Journal_Utilities
• .github/workflows/journal-integrity.yml line 21: repository: ActiveInferenceInstitute/Journal-Utilities → ActiveInferenceInstitute/Journal_Utilities

Until then, both workflows keep working only because the old repo name redirects — but actions/checkout does not follow redirects, so these MUST be merged promptly (CI will fail on the legacy name).

Intentionally left unchanged

• Prose product-name references ("Generated by Journal-Utilities", step names, path shorthand like Journal-Utilities/scripts/...) and local checkout path: names — not URL references
• REVIEW_LOG_2026-08-02.md, TO-DO.md — historical review notes
• trace.txt local machine paths (/mnt/md0/projects/Journal-Utilities/...) — historical run traces
• No issues/<n> or pull/<n> deep links referencing the old name were found in this repo

Old URLs redirect automatically. Migration context: https://github.com/ActiveInferenceInstitute/nest-internal/blob/main/governance/github-org-migration.md

[docxology]

Workflow lines added by the operator (the sweep PAT lacked workflow scope, commit aa6d7cf): actions/checkout repository: in deploy-pages.yml and journal-integrity.yml now point at Journal_Utilities.