diff --git a/run.json b/run.json
index 0aaf58567..e958b3fa1 100644
--- a/run.json
+++ b/run.json
@@ -248,7 +248,7 @@
     "kind": "running"
   },
   "status_updated_at": "2026-07-01T17:04:28.408821158Z",
-  "last_event_at": "2026-07-01T17:06:30.397674241Z",
+  "last_event_at": "2026-07-01T17:06:34.290348025Z",
   "pending_control": null,
   "checkpoints": [
     {
@@ -289,9 +289,9 @@
       "diff": {}
     },
     {
-      "seq": 0,
+      "seq": 113,
       "checkpoint": {
-        "timestamp": "2026-07-01T17:06:30.452646582Z",
+        "timestamp": "2026-07-01T17:06:34.290020974Z",
         "current_node": "patch",
         "completed_nodes": [
           "start",
@@ -299,24 +299,24 @@
         ],
         "node_retries": {},
         "context_values": {
+          "internal.thread_id": "start",
           "internal.node_visit_count": 1,
+          "response.patch": "I've hit a hard blocker and cannot make progress on this task. Here's the precise diagnosis:\n\n## Blocker: no GitHub access + shell is unusable\n\nEvery shell invocation — even `echo hello` — fails before executing, with:\n\n```\nfailed to mint GitHub installation access token:\nGitHub App does not have access to repository fabro.\nUpdate the installation's repository permissions to include it.\n```\n\nThis is fatal for this specific goal, because \"triage Dependabot alerts and open verified patch PRs\" depends entirely on things I now can't do:\n\n| Step | Requires | Status |\n|------|----------|--------|\n| List Dependabot alerts | Authenticated GitHub Security API (`security_events: read`) | ❌ no token / no repo access |\n| Create branch, commit, push | `git` via shell + repo write | ❌ shell blocked, no access |\n| Open PRs | GitHub PR API (`pull_requests: write`) | ❌ no access |\n| Verify fixes (`cargo build`, `cargo nextest`) | shell | ❌ shell blocked |\n\nI also confirmed the `eng-patch-cves` skill definition is **not present in the working tree** (`grep` for `patch-cves`, `eng-patch`, `dependabot`, and `cve` finds nothing relevant), even though commit `943dbe224` claims to add it. So I can't recover the exact workflow steps locally either. `read_file` and `grep` work, but `shell` and recursive `glob` are broken in this environment.\n\n## What I did *not* do\n\nI did not fabricate any alerts, branches, or PRs. Nothing was changed.\n\n## What needs to happen to unblock\n\n1. **Grant the GitHub App installation access to the `fabro` repository** (the error message says this directly). The installation needs, at minimum:\n   - `security_events: read` (to read Dependabot alerts)\n   - `contents: write` + `pull_requests: write` (to push branches and open PRs)\n2. **Restore shell execution** — the token-minting failure is happening at the shell-tool wrapper layer and blocks *all* commands, not just GitHub ones. This looks like an infrastructure/credential configuration issue in the run environment rather than something I can fix from inside the workspace.\n\n## How would you like to proceed?\n\n- If you can fix the installation permissions and shell access, re-run `/eng-patch-cves` and I'll do the full triage-and-PR flow.\n- Alternatively, if you paste the current Dependabot alert list here, I can prepare the dependency-bump edits locally (e.g., `Cargo.toml` / `bun.lock` changes) so they're ready to push once access is restored — though I still couldn't verify builds without shell.\n\nWhich do you prefer?",
           "internal.retry_count.patch": 0,
           "internal.retry_count.start": 0,
-          "internal.run_id": "01KWFA6TC0GC574MQMR4E0MV5D",
-          "internal.fidelity": "compact",
-          "outcome": "succeeded",
-          "graph.goal": "Triage GitHub Dependabot alerts and open verified dependency-patch PRs",
-          "thread.start.current_node": "patch",
-          "last_response": "I've hit a hard blocker and cannot make progress on this task. Here's the precise diagnosis:\n\n## Blocker: no GitHub access + shell is unusable\n\nEvery shell invocation — even `echo hello` — fails b",
-          "response.patch": "I've hit a hard blocker and cannot make progress on this task. Here's the precise diagnosis:\n\n## Blocker: no GitHub access + shell is unusable\n\nEvery shell invocation — even `echo hello` — fails before executing, with:\n\n```\nfailed to mint GitHub installation access token:\nGitHub App does not have access to repository fabro.\nUpdate the installation's repository permissions to include it.\n```\n\nThis is fatal for this specific goal, because \"triage Dependabot alerts and open verified patch PRs\" depends entirely on things I now can't do:\n\n| Step | Requires | Status |\n|------|----------|--------|\n| List Dependabot alerts | Authenticated GitHub Security API (`security_events: read`) | ❌ no token / no repo access |\n| Create branch, commit, push | `git` via shell + repo write | ❌ shell blocked, no access |\n| Open PRs | GitHub PR API (`pull_requests: write`) | ❌ no access |\n| Verify fixes (`cargo build`, `cargo nextest`) | shell | ❌ shell blocked |\n\nI also confirmed the `eng-patch-cves` skill definition is **not present in the working tree** (`grep` for `patch-cves`, `eng-patch`, `dependabot`, and `cve` finds nothing relevant), even though commit `943dbe224` claims to add it. So I can't recover the exact workflow steps locally either. `read_file` and `grep` work, but `shell` and recursive `glob` are broken in this environment.\n\n## What I did *not* do\n\nI did not fabricate any alerts, branches, or PRs. Nothing was changed.\n\n## What needs to happen to unblock\n\n1. **Grant the GitHub App installation access to the `fabro` repository** (the error message says this directly). The installation needs, at minimum:\n   - `security_events: read` (to read Dependabot alerts)\n   - `contents: write` + `pull_requests: write` (to push branches and open PRs)\n2. **Restore shell execution** — the token-minting failure is happening at the shell-tool wrapper layer and blocks *all* commands, not just GitHub ones. This looks like an infrastructure/credential configuration issue in the run environment rather than something I can fix from inside the workspace.\n\n## How would you like to proceed?\n\n- If you can fix the installation permissions and shell access, re-run `/eng-patch-cves` and I'll do the full triage-and-PR flow.\n- Alternatively, if you paste the current Dependabot alert list here, I can prepare the dependency-bump edits locally (e.g., `Cargo.toml` / `bun.lock` changes) so they're ready to push once access is restored — though I still couldn't verify builds without shell.\n\nWhich do you prefer?",
-          "current_node": "patch",
-          "graph.model_stylesheet": "\n            * { model: claude-opus-4-8; }\n        ",
-          "internal.thread_id": "start",
-          "failure_signature": "",
           "last_stage": "patch",
-          "graph.rankdir": "LR",
+          "internal.fidelity": "compact",
           "internal.work_dir": "/home/daytona/workspace/fabro",
-          "failure_class": ""
+          "graph.goal": "Triage GitHub Dependabot alerts and open verified dependency-patch PRs",
+          "graph.model_stylesheet": "\n            * { model: claude-opus-4-8; }\n        ",
+          "thread.start.current_node": "patch",
+          "outcome": "succeeded",
+          "current_node": "patch",
+          "failure_class": "",
+          "graph.rankdir": "LR",
+          "internal.run_id": "01KWFA6TC0GC574MQMR4E0MV5D",
+          "last_response": "I've hit a hard blocker and cannot make progress on this task. Here's the precise diagnosis:\n\n## Blocker: no GitHub access + shell is unusable\n\nEvery shell invocation — even `echo hello` — fails b",
+          "failure_signature": ""
         },
         "node_outcomes": {
           "patch": {
@@ -363,15 +363,68 @@
           }
         },
         "next_node_id": "exit",
+        "git_commit_sha": "b0f3337ec44c0b52faa72c7d31242cb2d96a06f3",
         "node_visits": {
           "start": 1,
           "patch": 1
         }
       },
-      "diff": {}
+      "diff": {
+        "summary": {
+          "files_changed": 0,
+          "additions": 0,
+          "deletions": 0
+        }
+      }
     }
   ],
-  "conclusion": null,
+  "conclusion": {
+    "timestamp": "2026-07-01T17:06:34.303984498Z",
+    "status": "succeeded",
+    "timing": {
+      "wall_time_ms": 125884,
+      "inference_time_ms": 118559,
+      "tool_time_ms": 1500,
+      "active_time_ms": 120059
+    },
+    "final_git_commit_sha": "b0f3337ec44c0b52faa72c7d31242cb2d96a06f3",
+    "stages": [
+      {
+        "stage_id": "start",
+        "stage_label": "start",
+        "timing": {
+          "wall_time_ms": 0,
+          "inference_time_ms": 0,
+          "tool_time_ms": 0,
+          "active_time_ms": 0
+        },
+        "retries": 0
+      },
+      {
+        "stage_id": "patch",
+        "stage_label": "patch",
+        "timing": {
+          "wall_time_ms": 120477,
+          "inference_time_ms": 118559,
+          "tool_time_ms": 1500,
+          "active_time_ms": 120059
+        },
+        "billing_usd_micros": 715393,
+        "retries": 0
+      }
+    ],
+    "billing": {
+      "input_tokens": 22141,
+      "output_tokens": 7354,
+      "total_tokens": 368405,
+      "reasoning_tokens": 0,
+      "cache_read_tokens": 295191,
+      "cache_write_tokens": 43719,
+      "total_usd_micros": 715393
+    },
+    "total_retries": 0,
+    "diff": {}
+  },
   "sandbox": {
     "kind": "ready",
     "plan": {
@@ -401,7 +454,12 @@
       "first_event_seq": 22,
       "prompt": null,
       "response": null,
-      "completion": null,
+      "completion": {
+        "outcome": "succeeded",
+        "notes": "Stage completed: patch",
+        "failure_reason": null,
+        "timestamp": "2026-07-01T17:06:30.452392480Z"
+      },
       "provider_used": {
         "mode": "agent",
         "provider": "anthropic",
@@ -414,6 +472,12 @@
       "output": null,
       "started_at": "2026-07-01T17:04:29.974827713Z",
       "handler": "agent",
+      "timing": {
+        "wall_time_ms": 120477,
+        "inference_time_ms": 118559,
+        "tool_time_ms": 1500,
+        "active_time_ms": 120059
+      },
       "usage": {
         "input_tokens": 22141,
         "output_tokens": 7354,
@@ -622,7 +686,41 @@
         ],
         "warnings": []
       },
-      "state": "running"
+      "state": "succeeded"
+    },
+    "exit@1": {
+      "first_event_seq": 116,
+      "prompt": null,
+      "response": null,
+      "completion": {
+        "outcome": "succeeded",
+        "notes": null,
+        "failure_reason": null,
+        "timestamp": "2026-07-01T17:06:34.290348025Z"
+      },
+      "provider_used": null,
+      "diff": null,
+      "script_invocation": null,
+      "script_timing": null,
+      "parallel_results": null,
+      "output": null,
+      "started_at": "2026-07-01T17:06:34.290254352Z",
+      "handler": "exit",
+      "timing": {
+        "wall_time_ms": 0,
+        "inference_time_ms": 0,
+        "tool_time_ms": 0,
+        "active_time_ms": 0
+      },
+      "usage": {
+        "input_tokens": 0,
+        "output_tokens": 0,
+        "total_tokens": 0,
+        "reasoning_tokens": 0,
+        "cache_read_tokens": 0,
+        "cache_write_tokens": 0
+      },
+      "state": "succeeded"
     },
     "start@1": {
       "first_event_seq": 18,
diff --git a/stages/002-patch@1/status.json b/stages/002-patch@1/status.json
new file mode 100644
index 000000000..da60ed32c
--- /dev/null
+++ b/stages/002-patch@1/status.json
@@ -0,0 +1,6 @@
+{
+  "outcome": "succeeded",
+  "notes": "Stage completed: patch",
+  "failure_reason": null,
+  "timestamp": "2026-07-01T17:06:30.452392480Z"
+}
\ No newline at end of file
diff --git a/stages/003-exit@1/status.json b/stages/003-exit@1/status.json
new file mode 100644
index 000000000..5b9eda081
--- /dev/null
+++ b/stages/003-exit@1/status.json
@@ -0,0 +1,6 @@
+{
+  "outcome": "succeeded",
+  "notes": null,
+  "failure_reason": null,
+  "timestamp": "2026-07-01T17:06:34.290348025Z"
+}
\ No newline at end of file