Update ID format to use per-repo prefixes and random suffix
Migrated all issue, TODO, and decision IDs to a new 4-part format: <PREFIX>-<TOPIC>-<TYPE>-<RAND>. Added per-repo prefix declarations in copilot-instructions.md and documented conventions in REPO_PREFIXES.md. Updated all topic registries, logs, cross-references, and documentation to use the new format. Introduced MIGRATION_ID_MAPPING.md for old-to-new ID mapping. Enhanced skills and protocol audit logic to validate and enforce per-repo prefixes and topic codes at runtime. Clarified Framework-First doctrine and ensured all references are unambiguous.
ADR skill, status vocab, and security log fixes
- Enhanced `adr-author` skill and ADR template based on first use: clarified opinion sharing, cross-referencing, index updates, and parallel session handling; rewrote ADR template pointer and added first repo-wide ADR.
- Updated skill loading: only `docs-discovery` and `docs-check` pre-loaded; others lazy-loaded; removed `version` from SKILL.md frontmatters.
- Simplified issue/TODO status to `Open`, `InProgress`, `Closed`; updated archiving logic and migrated all entries.
- Added forward-slash glob pattern rule to `docs-discovery/SKILL.md`.
- Closed LOG-I-9 and LOG-I-10: DEBUG-gated sensitive log lines, fixed typo, and cross-referenced new ADR.
- Various documentation and index improvements.
- Introduced the `adr-author` skill for structured ADR creation; updated session setup and shared skills to require pre-loading it.
- Added `SKILL.md` and `ADR_TEMPLATE.md` for ADR authoring workflow and documentation.
- Updated protocol decision log with entries for the new skill and its integration.
- Documented two critical JWT logging security issues in `LOGGING_ISSUES.md`.
- Minor: added a cleanup Bash command in `settings.local.json`.
Loretta