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planned "three-layer system" that was superseded by the current skills-based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
Remove cortex-workflow references since the command is not implemented
and workflow orchestration is currently handled through composition of
existing commands (agent, skills, review, plan, export, ai).
- Remove workflow subcommand from validation and generation
- Remove cortex-workflow.1 from manpage bundle
- Delete placeholder cortex-workflow.1 manpage file
This keeps the build clean and only bundles manpages for implemented
commands (cortex.1 and cortex-tui.1).
Nicholas Ferguson