V48: QA Deposit Clone-Vcs Agent End

Marker at refine/CS/structured_output (49 calls). Fix useTools hoist,
clone tool registration + git-https, PCC host ranking, thin VCS, and
workspacePath merge after tools. Ledger 1.D9 Accepted.

Author: geraldarthurdavis

.qa/BITCODE_V48_CANONICAL_PROMOTION_ACCEPTANCE.md

@@ -29,8 +29,8 @@
 
 | § | Topic | Status |
 | --- | --- | --- |
-| 1 | Every-call / every-pipeline LLM debug | **Partial** (read 1.1; deposit 1.D1–1.D8; **Try PCC reason**) |
-| 2 | SDIVF deposit pipeline production-like accept | **Partial** (clone-vcs Plan closed; Try PCC started) |
+| 1 | Every-call / every-pipeline LLM debug | **Partial** (read 1.1; deposit 1.D1–1.D9; **clone-vcs agent end**) |
+| 2 | SDIVF deposit pipeline production-like accept | **Partial** (clone-vcs Plan→Try→Retry→Refine closed at agent end) |
 | 3 | SDIVF read pipeline production-like accept | Open (partial offline via §1.1) |
 | 4 | Settle Simple pipeline production-like accept | Open |
 | 5 | Discovery law (wave-1 parallel → product search keys) | Open |
@@ -75,10 +75,11 @@ pnpm --filter @bitcode/pipeline-hosts run qa:read:debug-first-llm
 | `BITCODE_DEBUG_FORCE_CLONE_PTRR` | `1` | Force real clone PTRR agent |
 | `BITCODE_DEBUG_STOP_AFTER_FIRST_REASON` | `1` | Hard-stop **flag** name (historical); generation pin is separate |
 | `BITCODE_DEBUG_STOP_PHASE` | `setup` | |
-| `BITCODE_DEBUG_STOP_STEP` | **`try`** | progressive Try (after 1.D7 Plan close) |
-| `BITCODE_DEBUG_STOP_FAILSAFE` | **`prepare_concise_context`** | Try PCC selection |
-| `BITCODE_DEBUG_STOP_GENERATION` | **`reason`** | Try PCC reason (1.D8) |
+| `BITCODE_DEBUG_STOP_STEP` | **`refine`** | end of clone-vcs agent (after 1.D9) |
+| `BITCODE_DEBUG_STOP_FAILSAFE` | **`chunk_then_sum`** | Refine CS task SO |
+| `BITCODE_DEBUG_STOP_GENERATION` | **`structured_output`** | agent terminal task gen |
 | `BITCODE_DEBUG_STOP_AGENT_FILTER` | `clone-vcs` | |
+| `BITCODE_PIPELINE_HOST_MAX_RUNTIME_MS` | `900000` | full Plan+Try+Retry+Refine budget |
 | `BITCODE_LLM_PROVIDER` / `BITCODE_LLM_MODEL` | anthropic / `claude-haiku-4-5` | |
 
 **Artifact root:** `.tmp/llm-call-debug/<runId>/`  
@@ -1322,26 +1323,104 @@ Explicit: “No tools are invoked in this Reason generation.”
 
 | | |
 | --- | --- |
-| **this stop** | **Accepted** |
-| **next marker** | Try · prepare_concise_context · **judge** |
-| **not yet** | Try PCC SO → CS → useTools → clone tool; remaining Setup |
+| **this stop** | **Accepted** (historical) |
+| **next marker** | advanced → full agent end (see **1.D9**) |
+| **not yet** | (closed by 1.D9) remaining Setup agents |
 
 #### artifacts
 
 | Kind | Path |
 | --- | --- |
 | Request | `.tmp/llm-call-debug/…/0013-request-…-try-prepare_concise_context-reason.json` |
-| Response | `.tmp/llm-call-debug/…/0014-response-…-try-prepare_concise_context-reason.json` |
+| Response | `.tmp/llm-call-debug/…/0014-response-…-try-prepare_concise-context-reason.json` |
 | Abort | `.tmp/llm-call-debug/…/0015-abort-…-try-…-reason.json` |
 | Re-run | `pnpm --filter @bitcode/pipeline-hosts run qa:deposit:debug-first-llm` |
 
 ---
 
+### 1.D9 Deposit · Setup · clone-vcs · **Agent end** (Plan→Try→Retry→Refine CS SO)
+
+- **status:** **Accepted (clone-vcs agent complete under progressive marker)**
+- **date:** 2026-07-16
+- **commit_tag:** `QA Pipeline Deposit Phase Setup Agent Clone-Vcs Agent End Plan Try Retry Refine`
+- **pipeline:** `ExecutionPipelineSDIVFSynthesizeDepositAssetPacks`
+- **phase:** setup
+- **agent:** `asset-pack-clone-vcs-repository-agent`
+- **step / failsafe / thinking (stop):** **refine** / **chunk_then_sum** / **structured_output**
+- **execution_path (abort):**
+  `…/agent:asset-pack-clone-vcs-repository-agent → refine → failsafe:chunk_then_sum → gen-0 → seq-2 → thinkings:structured_output`
+- **provider / model:** anthropic / `claude-haiku-4-5`
+- **harness:** `ok: true`, `debugStop: true`, **`callCount: 49`**, stopStep=`refine`, stopFailsafe=`chunk_then_sum`, stopGeneration=`structured_output`
+- **abort:** `hard-stop after refine/chunk_then_sum/structured_output agent=asset-pack-clone-vcs-repository-agent`
+
+#### coverage (single agent-end run)
+
+| PTRR step | PCC (R/J/SO) | CS (R/J/SO) | Tools postprocess |
+| --- | --- | --- | --- |
+| **Plan** | ✓ | ✓ PlanStepOutput (approach/steps) | none (correct) |
+| **Try** | ✓ | ✓ agent schema + **useTools** | **yes** — `asset-pack-clone-vcs-repository-tool` |
+| **Retry** | ✓ (includes try tools:used keys) | ✓ real `workspacePath` under `/var/folders/…/bitcode-clone-…` | yes when selected |
+| **Refine** | ✓ | ✓ agent return (stop here) | none (correct; no postprocess) |
+
+Stitch: non-triggering (schema-valid CS SO; stitchCount=0).
+
+#### critique → fix (this agent session)
+
+| Defect | Fix |
+| --- | --- |
+| VCS system “DevOps soup” (Jenkins/Gerrit) | Thin Host-bound VCS prose |
+| PCC ranking preferred null deposit shells | Prefer `#host:sourceRevision` / workspace; Plan PCC SO now selects host keys first |
+| Try/Retry `useTools` never executed | (1) hoist `reasoning.useTools` → tools postprocess; (2) add optional `useTools` on clone agent schema; (3) **tool not registered** — missing `__docCodePrompt` aborted whole tool loop; per-tool fail-soft + attach prompt |
+| Clone tool `undefined.length` on agent-shaped input | Rewrite AssetPack clone tool to accept `{provider,owner,name,ref}` and git-https clone |
+| Try SO stuck pre-tool | Tools postprocess folds successful `workspacePath` into step `output` |
+| Settlement/delivery on synth | Already purged (no `settleDelivery` / `settlementBoundary` on wire) |
+
+#### excellence (agent end)
+
+| Axis | Result |
+| --- | --- |
+| **hierarchy** | **Pass** — Pipeline→Phase→Agent→Step→Failsafe→Thinking; Execution once |
+| **dual law** | **Pass** — PCC keys-only user; CS prepared `selectedKeys`+`selectedContext` |
+| **useTools law** | **Pass** — Plan/PCC omit; Try reason+SO select catalog tool; Refine no postprocess |
+| **tools execute** | **Pass** — postprocess runs; real temp workspace from clone tool |
+| **settle ban** | **Pass** — no settleDelivery on synth wire |
+| **prompt hygiene** | **Pass** — thin VCS; no Jenkins soup |
+
+#### residual (non-blocking for agent-end accept)
+
+- Refine CS may still invent wrong tool name (`cloneRepositoryTool`) or pending status in SO text (no tools postprocess on Refine — final return quality, not execution).  
+- Thin VCS string intermittent on some system walks (agent still has VCS Operations identity).  
+- Many non-clone tools still lack `__docCodePrompt` (logged skip at preprocess; catalog partially populated).  
+- Next progressive marker: next Setup agent or Discovery (not further clone-vcs gens).
+
+#### stability_confidence
+
+- **0.90** that clone-vcs agent end (Plan→Try→Retry→Refine CS SO, 49 calls, tools postprocess) is successful for V48 progressive deposit QA.
+
+#### decision
+
+| | |
+| --- | --- |
+| **this stop** | **Accepted — clone-vcs agent complete** |
+| **next marker** | next Setup agent **or** Discovery (leave refine/CS/SO until next agent starts) |
+| **not yet** | initialize-lsp / mcps / comprehend-obfuscations / danger-wall; Discovery |
+
+#### artifacts
+
+| Kind | Path |
+| --- | --- |
+| Work root | `.tmp/local-deposit-debug/` |
+| Wire report | `.tmp/llm-call-debug/pipeline-synthesize_deposit_asset_packs/VERBATIM_WIRE_REPORT.md` |
+| Ledger | `…/ledger.jsonl` (49 entries) |
+| Abort | `…/0049-abort-…-refine-chunk_then_sum-structured_output.json` |
+| Re-run | `pnpm --filter @bitcode/pipeline-hosts run qa:deposit:debug-first-llm` |
+
+---
+
 ### 1.2+ Read next / Deposit next
 
-- **1.D9** Deposit · Setup · clone-vcs · **Try** · PCC · **judge**  
+- **1.D10** next Setup agent (or Discovery) — progressive marker  
 - **1.2** Read · Setup · clone-vcs · Plan · PCC · **judge**  
-- **1.D10+** Try PCC SO → CS → tools/clone; remaining Setup; Discovery · …  
 
 ---
 
@@ -1351,8 +1430,8 @@ Explicit: “No tools are invoked in this Reason generation.”
 
 - **status:** **Partial**  
 - **criterion:** full Setup→…→Finish deposit run under LocalHost / production-like accept with real inference; until then, §1 deposit call-by-call rows are the progressive proof.  
-- **proof (current):** §1.D1–1.D7 Plan complete; §1.D8 Try PCC reason Accepted.  
-  `pnpm --filter @bitcode/pipeline-hosts run qa:deposit:debug-first-llm` → `debugStop: true`, stopStep=`try`, stopGeneration=`reason`, callCount=15.
+- **proof (current):** §1.D1–1.D9 **clone-vcs agent complete** (Plan→Try→Retry→Refine, tools postprocess, callCount=49).  
+  `pnpm --filter @bitcode/pipeline-hosts run qa:deposit:debug-first-llm` → `debugStop: true`, stopStep=`refine`, stopFailsafe=`chunk_then_sum`, stopGeneration=`structured_output`.
 
 ### §3 SDIVF read pipeline production-like accept
 
@@ -1418,3 +1497,4 @@ Explicit: “No tools are invoked in this Reason generation.”
 | --- | --- |
 | 2026-07-16 | Document created. §1 method + entry **1.1** (read clone Plan PCC reason) filled from live `pnpm run debug:read:first-llm` after commits retiring substeps, PTRR order, and PCC prompt work. |
 | 2026-07-16 | §7 retitled: Host selection (API/dispatch) **vs** SDIVF Setup phase — naming clarification only; no host-selection bug found in read synthesize path from this audit. |
+| 2026-07-16 | **1.D9** clone-vcs agent end Accepted: marker refine/CS/SO; useTools hoist + clone tool registration/git-https; tools postprocess merges workspacePath. |

packages/agent-generics/src/__tests__/step-postprocess-tools.test.ts

@@ -24,4 +24,32 @@ describe('Tools execute as Step postprocess once', () => {
 
     spy.mockRestore();
   });
+
+  it('runs tools when useTools is only on reasoning (SO omitted)', async () => {
+    const generationFactories = require('../generations/llm-bound-factories');
+    const spy = jest.spyOn(generationFactories, 'factoryToolsExecution').mockImplementation(() => {
+      return async (input: any) => ({ ...input, usedTools: [{ tool: 'from-reason' }] });
+    });
+
+    const step = factoryTryStep<any, any>({ parse: (x: any) => x } as any);
+    const exec = new Execution('agent-root');
+
+    const out = await step(
+      {
+        output: { success: false },
+        reasoning: {
+          analysis: 'need clone',
+          reasoningItems: [],
+          conclusion: 'run tool',
+          confidence: 0.9,
+          useTools: [{ name: 'asset-pack-clone-vcs-repository-tool', input: { owner: 'o', name: 'n' } }],
+        },
+      },
+      exec as any,
+    );
+    expect(spy).toHaveBeenCalled();
+    expect(out.usedTools).toEqual([{ tool: 'from-reason' }]);
+
+    spy.mockRestore();
+  });
 });

packages/agent-generics/src/__tests__/tool-hierarchy-cross-registry.test.ts

@@ -0,0 +1,78 @@
+// @ts-nocheck
+/**
+ * Cross-registry tool lookup: pipeline ExecutionPipelineToolRegistry
+ * must be visible from StepExecution AgentToolsRegistry after restrictTo.
+ */
+import { Execution } from '@bitcode/execution-generics';
+import { Tool } from '@bitcode/tools-generics';
+import { AgentExecution, StepExecution, applyStepToolSurface } from '../execution';
+import { factoryToolsExecution } from '../generations/llm-bound-factories';
+
+class CloneTool extends Tool {
+  name = 'asset-pack-clone-vcs-repository-tool';
+  use = jest.fn(async (input: any) => ({ ok: true, input }));
+}
+
+/** Minimal stand-in for ExecutionPipelineToolRegistry (same surface). */
+class FakePipelineTools {
+  private map = new Map<string, any>();
+  constructor(public execution: any) {}
+  registerTool(key: string, tool: any) { this.map.set(key, tool); }
+  get(key: string) { return this.map.get(key); }
+  getTool(key: string) { return this.map.get(key); }
+  getPaths() { return [...this.map.keys()]; }
+  getUsableTools() {
+    const o: any = {};
+    for (const k of this.map.keys()) o[k] = this.map.get(k);
+    return o;
+  }
+}
+
+describe('cross-registry tool hierarchy', () => {
+  it('step getTool finds pipeline-registered tool under restrictTo', () => {
+    const pipeline = new Execution('pipeline') as any;
+    pipeline.tools = new FakePipelineTools(pipeline);
+    const clone = new CloneTool();
+    pipeline.tools.registerTool('asset-pack-clone-vcs-repository-tool', clone);
+
+    const agent = new AgentExecution('agent:clone', pipeline);
+    const tryStep = new StepExecution('try', agent);
+    applyStepToolSurface(tryStep, ['asset-pack-clone-vcs-repository-tool']);
+
+    expect(tryStep.tools.getTool('asset-pack-clone-vcs-repository-tool')).toBeTruthy();
+    expect(Object.keys(tryStep.tools.getUsableTools())).toEqual([
+      'asset-pack-clone-vcs-repository-tool',
+    ]);
+  });
+
+  it('tools postprocess on sequential child still finds tool', async () => {
+    const pipeline = new Execution('pipeline') as any;
+    pipeline.tools = new FakePipelineTools(pipeline);
+    const clone = new CloneTool();
+    pipeline.tools.registerTool('asset-pack-clone-vcs-repository-tool', clone);
+
+    const agent = new AgentExecution('agent:clone', pipeline);
+    const tryStep = new StepExecution('try', agent);
+    applyStepToolSurface(tryStep, ['asset-pack-clone-vcs-repository-tool']);
+
+    // Mimic sequential(core, tools) → tools runs on child seq-1
+    const seq1 = tryStep.child('seq-1');
+    const toolsExec = factoryToolsExecution();
+    const out = await toolsExec(
+      {
+        output: {
+          useTools: [
+            {
+              name: 'asset-pack-clone-vcs-repository-tool',
+              input: { owner: 'a', name: 'b' },
+            },
+          ],
+        },
+      },
+      seq1 as any,
+    );
+    expect(out.usedTools?.[0]?.error).toBeUndefined();
+    expect(out.usedTools?.[0]?.tool).toBe('asset-pack-clone-vcs-repository-tool');
+    expect(clone.use).toHaveBeenCalled();
+  });
+});