Feat/host orchestrator durable session

.gitignore

@@ -27,3 +27,6 @@ docs/project_management/packs/**/logs/
 .mcp.json
 .DS_Store
 **/.DS_Store
+.gitnexus
+.orchestrator-*
+.substrate

AGENTS.md

@@ -37,7 +37,7 @@ cargo clippy --workspace --all-targets -- -D warnings
 cargo test --workspace -- --nocapture       # run full suite with output
 cargo bench                                 # exercise hotspots when touching performance-sensitive crates
 ```
-- Avoid `--all-features` at the workspace level; enable graph features explicitly (e.g., `cargo build -p substrate-graph --features kuzu-dylib`).
+- Avoid `--all-features` at the workspace level; enable graph features explicitly via the graph crate manifest (e.g., `cargo build --manifest-path crates/substrate-graph/Cargo.toml --features kuzu-dylib`).
 - Regenerate shims for manual testing with `substrate --shim-deploy`; inspect with `substrate --shim-status`.
 
 ## Coding Standards & Patterns
@@ -91,3 +91,47 @@ cargo bench                                 # exercise hotspots when touching pe
 - `scripts/dev-entrypoint.sh`: reproducible dev container bootstrap.
 - `docs/BACKLOG.md`: living backlog for DX improvements/bugs.
 - Update these guides when behavior changes; stale docs are treated as regressions.
+
+<!-- gitnexus:start -->
+# GitNexus — Code Intelligence
+
+This project is indexed by GitNexus as **substrate** (46052 symbols, 69611 relationships, 300 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+
+> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+
+## Always Do
+
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+
+## Never Do
+
+- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
+- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
+- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+
+## Resources
+
+| Resource | Use for |
+|----------|---------|
+| `gitnexus://repo/substrate/context` | Codebase overview, check index freshness |
+| `gitnexus://repo/substrate/clusters` | All functional areas |
+| `gitnexus://repo/substrate/processes` | All execution flows |
+| `gitnexus://repo/substrate/process/{name}` | Step-by-step execution trace |
+
+## CLI
+
+| Task | Read this skill file |
+|------|---------------------|
+| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
+| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
+| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
+| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
+
+<!-- gitnexus:end -->

CLAUDE.md

@@ -0,0 +1,43 @@
+<!-- gitnexus:start -->
+# GitNexus — Code Intelligence
+
+This project is indexed by GitNexus as **substrate** (46052 symbols, 69611 relationships, 300 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+
+> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+
+## Always Do
+
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+
+## Never Do
+
+- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
+- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
+- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
+- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
+
+## Resources
+
+| Resource | Use for |
+|----------|---------|
+| `gitnexus://repo/substrate/context` | Codebase overview, check index freshness |
+| `gitnexus://repo/substrate/clusters` | All functional areas |
+| `gitnexus://repo/substrate/processes` | All execution flows |
+| `gitnexus://repo/substrate/process/{name}` | Step-by-step execution trace |
+
+## CLI
+
+| Task | Read this skill file |
+|------|---------------------|
+| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
+| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
+| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
+| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
+| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
+| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
+
+<!-- gitnexus:end -->