Nicholas Ferguson 0348090e39 docs: remove phantom feature references and fix stale documentation ...

Remove references to non-existent modes/, workflows/, profiles/, scenarios/,
and flags/ directories across 11 documentation files. These described a
planned "three-layer system" that was superseded by the current skills-based
architecture.

Key changes:
- AGENTS.md: update core module tree to match actual codebase
- docs/index.md: fix version (2.0.0 → 3.0.1), remove Mode/Workflow/Flag sections
- docs/guides/hooks.md: replace 7 phantom hooks with 9 actual hooks
- docs/reference/api/index.md: list actual core modules
- docs/reference/architecture/: remove three-layer references, fix paths
- Archive quick-reference.md (entirely phantom content)
- Fix broken modes.html links and stale CLI command references

2026-03-06 15:05:47 -05:00

..

index.md

docs: remove phantom feature references and fix stale documentation

2026-03-06 15:05:47 -05:00

installer.md

docs: fix outdated references and rewrite INSTALL.md

2026-02-16 10:23:33 -05:00