Refactor documentation links for consistency and clarity
- Updated internal links in various security and runtime documentation to remove redundant paths and ensure they point to the correct sections.
- Adjusted references in the Project Trust, Extension Integrity, Extension Isolation, LLM Context Isolation, MCP Trust, Secrets Hygiene, Security Modes, Tool Approvals, and Trust Model documents.
- Ensured all links are relative and consistent with the current documentation structure.
Wiki gap review: shapes, flows, reference extensions, Mermaid fixes
Pass 1–4 of the post-codex gap review:
- Glossary: add envelope; strengthen turn-stage / SM-stage disambiguation; add minor terms.
- StageContext expanded in SM-Stage-Lifecycle; cross-linked from Context-Assembly.
- Context-Providers fix: hooks may introduce new request content (align with Message-Loop).
- Settings-Shape, Extension-Installation, Launch-Arguments, Network-Policy, Platform-Integration added.
- Error-Model: core-default retry/backoff; adapter override framing.
- Session-Manifest: manifestVersion + forward/backward-compat rules.
- Persistence-and-Recovery: no auto-GC; retention is per Session Store.
- Hook-Taxonomy: canonical 12-slot matrix + per-slot ordering flowchart.
- Reference extensions: File logger, CLI-Wrapper provider, three example hooks, SystemPromptFile CP.
- Seven new flows: First-Run, SM-Stage-Retry, Guard-Deny-Reproposal, Reload-Mid-Turn, Interaction-Timeout, MCP-Reconnect, Session-Resume-Drift, Compaction-Warning.
- Two MCP flows: MCP-Prompt-Consume, MCP-Resource-Bind.
- Mermaid polish: quote sequence-diagram messages with braces / multi-colons; quote flowchart node labels with colons; quote risky participant aliases.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>