Full-repo sweep remediation: 44 fixes, stack-graphs rip, read-only MCP surface

.claude/agents/code-analyst.md

@@ -1,7 +1,7 @@
 ---
 name: code-analyst
 description: Use when the user asks to understand code structure, impact of changes, find owners, audit dependencies, or navigate the codebase graph. Specializes in the OpenCodeHub MCP toolkit and always grounds claims in graph queries rather than text search.
-tools: mcp__opencodehub__query, mcp__opencodehub__context, mcp__opencodehub__impact, mcp__opencodehub__route_map, mcp__opencodehub__api_impact, mcp__opencodehub__shape_check, mcp__opencodehub__tool_map, mcp__opencodehub__verdict, mcp__opencodehub__owners, mcp__opencodehub__license_audit, mcp__opencodehub__list_findings, mcp__opencodehub__list_findings_delta, mcp__opencodehub__list_dead_code, mcp__opencodehub__signature, mcp__opencodehub__detect_changes, mcp__opencodehub__rename, Read, Grep, Glob
+tools: mcp__opencodehub__query, mcp__opencodehub__context, mcp__opencodehub__impact, mcp__opencodehub__route_map, mcp__opencodehub__api_impact, mcp__opencodehub__shape_check, mcp__opencodehub__tool_map, mcp__opencodehub__verdict, mcp__opencodehub__owners, mcp__opencodehub__license_audit, mcp__opencodehub__list_findings, mcp__opencodehub__list_findings_delta, mcp__opencodehub__list_dead_code, mcp__opencodehub__signature, mcp__opencodehub__detect_changes, Read, Grep, Glob
 model: sonnet
 ---
 
@@ -12,7 +12,7 @@ Tool selection rules:
 - **Impact / "what breaks if I change X"**: `impact` with `direction: "upstream"` for callers, `"downstream"` for callees; `api_impact` for public API boundaries; `shape_check` for structural drift across payloads and types.
 - **Ownership**: `owners` for top contributors. `signature` for canonical function signatures before quoting them.
 - **Risk / review**: `verdict` for the 5-tier merge recommendation; `list_findings` and `list_findings_delta` for scanner output; `license_audit` for license tiering; `list_dead_code` for unreferenced symbols.
-- **Refactors**: `rename` always with `dry_run: true` first — never apply without showing the diff and getting explicit confirmation.
+- **Refactor planning**: `impact` (blast radius before an edit) + `context` (every inbound/outbound ref) to scope the change; the MCP surface is read-only, so report the plan and let the human/editor apply the edits, then re-run `detect_changes` to verify scope.
 - **Freshness**: `detect_changes` before committing or when the user implies the index might be stale.
 
 Always cite with `path:line`. Never paraphrase signatures — quote them. If a tool returns nothing, say so; do not invent coverage.

.claude/skills/opencodehub-guide/SKILL.md

@@ -24,7 +24,7 @@ For any task that touches code understanding, debugging, impact analysis, refact
 | Understand architecture / "How does X work?"  | `opencodehub-exploring`       |
 | Blast radius / "What breaks if I change X?"   | `opencodehub-impact-analysis` |
 | Trace bugs / "Why is X failing?"              | `opencodehub-debugging`       |
-| Rename / extract / split / restructure        | `opencodehub-refactoring`     |
+| Plan a rename / extract / move (analysis only) | `opencodehub-refactoring`     |
 | Review a PR / "Is this safe to merge?"        | `opencodehub-pr-review`       |
 | Tools, resources, schema reference            | `opencodehub-guide` (here)    |
 
@@ -46,7 +46,9 @@ for the scope rationale.
 Fire these directly; do not nest them inside analysis skills. Each is a
 standalone artifact producer with its own preconditions and output path.
 
-## Tool Inventory (27 MCP tools)
+## Tool Inventory (28 MCP tools)
+
+> Every tool is **read-only with respect to your source**. No MCP tool edits the working tree; planning and verification tools surface what to change, and you (or your editor) apply the edit.
 
 ### Code intelligence (per-repo)
 
@@ -57,9 +59,8 @@ standalone artifact producer with its own preconditions and output path.
 | `mcp__opencodehub__context`           | 360-degree symbol view + `confidenceBreakdown` + `cochanges` side-section |
 | `mcp__opencodehub__impact`            | Blast radius with risk tier + `confidenceBreakdown`                       |
 | `mcp__opencodehub__detect_changes`    | Map an uncommitted or committed diff to affected symbols and flows        |
-| `mcp__opencodehub__rename`            | Graph-assisted multi-file rename; dry-run by default                      |
 | `mcp__opencodehub__sql`               | Read-only query: `sql` arg → temporal DuckDB (cochanges/summaries); `cypher` arg → lbug graph (5 s timeout) |
-| `mcp__opencodehub__signature`         | Function signature lookup for a target symbol                             |
+| `mcp__opencodehub__signature`         | Symbol declaration + stubbed members (class/interface header + method/property signatures, bodies elided) |
 
 ### HTTP / RPC surface
 
@@ -78,6 +79,8 @@ standalone artifact producer with its own preconditions and output path.
 | `mcp__opencodehub__group_query`       | BM25 fan-out across a group with reciprocal-rank fusion                   |
 | `mcp__opencodehub__group_status`      | Per-repo staleness + contract freshness for a group                       |
 | `mcp__opencodehub__group_contracts`   | HTTP contract cross-links (consumer FETCHES edge → producer Route)        |
+| `mcp__opencodehub__group_cross_repo_links` | Audit trail of every typed cross-repo edge, both endpoints `repo_uri`-qualified |
+| `mcp__opencodehub__group_sync`        | Rebuild the cross-repo contract registry + link table after a re-index    |
 
 ### Supply-chain / PR review (OpenCodeHub differentiators)
 
@@ -87,13 +90,13 @@ standalone artifact producer with its own preconditions and output path.
 | `mcp__opencodehub__scan`                 | Run Priority-1 scanners (openWorld — spawns child processes)           |
 | `mcp__opencodehub__list_findings`        | Browse SARIF findings produced by `scan` or `ingest-sarif`             |
 | `mcp__opencodehub__list_findings_delta`  | Diff latest scan vs. frozen baseline (new / fixed / unchanged / updated) |
-| `mcp__opencodehub__list_dead_code`       | Unreferenced exported symbols                                          |
-| `mcp__opencodehub__remove_dead_code`     | Scripted removal of dead-code items (dry-run by default)               |
+| `mcp__opencodehub__list_dead_code`       | Unreferenced exported symbols (read-only listing — you delete them)    |
 | `mcp__opencodehub__license_audit`        | Copyleft / unknown / proprietary tier check over dependencies          |
 | `mcp__opencodehub__dependencies`         | External package list (ecosystem + version + manifest path)            |
 | `mcp__opencodehub__owners`               | File/symbol ownership from CODEOWNERS + git blame signal               |
 | `mcp__opencodehub__risk_trends`          | Per-community trend lines and 30-day projections                       |
 | `mcp__opencodehub__project_profile`      | High-level repo summary (languages, stacks, entry points)              |
+| `mcp__opencodehub__pack_codebase`        | Deterministic LLM-ready code-pack snapshot of the repo                 |
 
 ## Differentiators to surface in responses
 
@@ -210,5 +213,5 @@ LIMIT 20;
 - Every per-repo tool accepts an optional `repo` argument. When exactly one repo is indexed, `repo` is optional. When two or more are indexed and `repo` is omitted, the tool returns `AMBIGUOUS_REPO` — pass `repo` explicitly.
 - Every response may carry `_meta.codehub/staleness` when the index is behind HEAD. Surface that to the user when it is present.
 - Every response includes a `next_steps` array under `structuredContent`. Use it to pick the next tool without guessing.
-- `rename` is dry-run by default — explicitly pass `dry_run: false` to apply edits.
+- No MCP tool edits user source. Tools like `impact`, `context`, and `detect_changes` tell you what a change touches; you (or your editor) make the edit, then re-run `detect_changes` to verify.
 - `scan` has `openWorldHint: true` — it spawns child processes. Do not invoke it on every turn.