diff --git a/run.json b/run.json
index 70bebc33e..0aaf58567 100644
--- a/run.json
+++ b/run.json
@@ -239,14 +239,138 @@
     }
   },
   "web_url": "https://fabro-testing.walleye-rainbow.ts.net/runs/01KWFA6TC0GC574MQMR4E0MV5D",
-  "start": null,
-  "status": {
-    "kind": "starting"
+  "start": {
+    "start_time": "2026-07-01T17:04:28.408788756Z",
+    "run_branch": "fabro/run/01KWFA6TC0GC574MQMR4E0MV5D",
+    "base_sha": "943dbe224a3a12cf993e443cc50a2e54f816cfa8"
   },
-  "status_updated_at": "2026-07-01T17:04:13.783168201Z",
-  "last_event_at": "2026-07-01T17:04:27.943769346Z",
+  "status": {
+    "kind": "running"
+  },
+  "status_updated_at": "2026-07-01T17:04:28.408821158Z",
+  "last_event_at": "2026-07-01T17:06:30.397674241Z",
   "pending_control": null,
-  "checkpoints": [],
+  "checkpoints": [
+    {
+      "seq": 21,
+      "checkpoint": {
+        "timestamp": "2026-07-01T17:04:29.974720466Z",
+        "current_node": "start",
+        "completed_nodes": [
+          "start"
+        ],
+        "node_retries": {},
+        "context_values": {
+          "internal.node_visit_count": 1,
+          "internal.thread_id": null,
+          "failure_class": "",
+          "graph.model_stylesheet": "\n            * { model: claude-opus-4-8; }\n        ",
+          "internal.retry_count.start": 0,
+          "current_node": "start",
+          "outcome": "succeeded",
+          "internal.work_dir": "/home/daytona/workspace/fabro",
+          "graph.rankdir": "LR",
+          "graph.goal": "Triage GitHub Dependabot alerts and open verified dependency-patch PRs",
+          "internal.fidelity": "compact",
+          "internal.run_id": "01KWFA6TC0GC574MQMR4E0MV5D",
+          "failure_signature": ""
+        },
+        "node_outcomes": {
+          "start": {
+            "status": "succeeded",
+            "usage": null
+          }
+        },
+        "next_node_id": "patch",
+        "node_visits": {
+          "start": 1
+        }
+      },
+      "diff": {}
+    },
+    {
+      "seq": 0,
+      "checkpoint": {
+        "timestamp": "2026-07-01T17:06:30.452646582Z",
+        "current_node": "patch",
+        "completed_nodes": [
+          "start",
+          "patch"
+        ],
+        "node_retries": {},
+        "context_values": {
+          "internal.node_visit_count": 1,
+          "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.work_dir": "/home/daytona/workspace/fabro",
+          "failure_class": ""
+        },
+        "node_outcomes": {
+          "patch": {
+            "status": "succeeded",
+            "context_updates": {
+              "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?",
+              "last_stage": "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"
+            },
+            "notes": "Stage completed: patch",
+            "usage": {
+              "input": {
+                "usage": {
+                  "model": {
+                    "provider": "anthropic",
+                    "model_id": "claude-opus-4-8"
+                  },
+                  "tokens": {
+                    "input_tokens": 22141,
+                    "output_tokens": 7354,
+                    "reasoning_tokens": 0,
+                    "cache_read_tokens": 295191,
+                    "cache_write_tokens": 43719
+                  }
+                },
+                "facts": {
+                  "algorithm": "anthropic",
+                  "cache_write_5m_tokens": 43719,
+                  "cache_write_1h_tokens": 0
+                }
+              },
+              "total_usd_micros": 715393
+            },
+            "timing": {
+              "wall_time_ms": 0,
+              "inference_time_ms": 118559,
+              "tool_time_ms": 1500,
+              "active_time_ms": 120059
+            }
+          },
+          "start": {
+            "status": "succeeded",
+            "usage": null
+          }
+        },
+        "next_node_id": "exit",
+        "node_visits": {
+          "start": 1,
+          "patch": 1
+        }
+      },
+      "diff": {}
+    }
+  ],
   "conclusion": null,
   "sandbox": {
     "kind": "ready",
@@ -272,5 +396,267 @@
   "pull_request": null,
   "superseded_by": null,
   "pending_interviews": {},
-  "stages": {}
+  "stages": {
+    "patch@1": {
+      "first_event_seq": 22,
+      "prompt": null,
+      "response": null,
+      "completion": null,
+      "provider_used": {
+        "mode": "agent",
+        "provider": "anthropic",
+        "model": "claude-opus-4-8"
+      },
+      "diff": null,
+      "script_invocation": null,
+      "script_timing": null,
+      "parallel_results": null,
+      "output": null,
+      "started_at": "2026-07-01T17:04:29.974827713Z",
+      "handler": "agent",
+      "usage": {
+        "input_tokens": 22141,
+        "output_tokens": 7354,
+        "total_tokens": 368405,
+        "reasoning_tokens": 0,
+        "cache_read_tokens": 295191,
+        "cache_write_tokens": 43719,
+        "total_usd_micros": 715393
+      },
+      "model": {
+        "provider": "anthropic",
+        "model_id": "claude-opus-4-8"
+      },
+      "permission_level": "full",
+      "agent_tools": [
+        {
+          "name": "AskUserQuestion",
+          "description": "Ask the human one or more questions and wait for their answers before continuing this stage.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "TaskCreate",
+          "description": "Create pending tasks in the current session. Use concise subjects, descriptions, optional activeForm text, and metadata. Check TaskList first to avoid duplicate tasks.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "TaskGet",
+          "description": "Get one task by taskId, including subject, status, description, owner, blockedBy, and blocks.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "TaskList",
+          "description": "List tasks for the current session, including status, owner, and blocking dependencies. Use TaskGet with a taskId for full description and dependency details.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "TaskUpdate",
+          "description": "Update an existing task's status, text, owner, metadata, or dependencies. Valid statuses are pending, in_progress, completed, and deleted. After completing a task, call TaskList to find newly unblocked work.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "close_agent",
+          "description": "Close a running subagent that is no longer needed.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "subagent",
+          "invoked": false
+        },
+        {
+          "name": "edit_file",
+          "description": "Edit a file by replacing an exact string. The old_string must be an exact match and unique unless replace_all is true; include surrounding context when needed. Read the file first and preserve existing indentation.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "write",
+          "invoked": false
+        },
+        {
+          "name": "glob",
+          "description": "Find files by file names using a glob pattern. Use path to choose the search root. Prefer this over shell find or ls when locating repository files.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "read",
+          "invoked": true
+        },
+        {
+          "name": "grep",
+          "description": "Search file contents with a regex pattern. Use path to choose the search root, glob_filter to limit matching files, case_insensitive for case folding, and max_results to cap output.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "read",
+          "invoked": true
+        },
+        {
+          "name": "read_file",
+          "description": "Read files before editing them. Returns line-numbered text and supports offset/limit for large files. Use this instead of shell cat, head, tail, or sed when inspecting repository files.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "read",
+          "invoked": true
+        },
+        {
+          "name": "send_input",
+          "description": "Send a follow-up message to a running subagent when new information or corrected instructions are needed.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "subagent",
+          "invoked": false
+        },
+        {
+          "name": "shell",
+          "description": "Execute shell commands for terminal operations, package managers, tests and builds. Use dedicated tools for file reads, file edits, filename searches, and content searches. Provide timeout_ms for long-running commands.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "shell",
+          "invoked": true
+        },
+        {
+          "name": "spawn_agent",
+          "description": "Spawn a subagent for independent work or context isolation. Use it for tasks that can proceed separately, and avoid duplicating the same work in the parent session.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "subagent",
+          "invoked": false
+        },
+        {
+          "name": "wait",
+          "description": "Wait for a subagent to complete, then use the result to synthesize the outcome for the user.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "subagent",
+          "invoked": false
+        },
+        {
+          "name": "web_fetch",
+          "description": "Fetch content from a URL that starts with http:// or https://. Pass a prompt to extract specific information or summarize the page; omit prompt to return the page content.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "web_search",
+          "description": "Search the web using Brave Search when current external information is needed. Returns result titles, URLs, and descriptions; use web_fetch for a specific URL.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "other",
+          "invoked": false
+        },
+        {
+          "name": "write_file",
+          "description": "Create new files, or overwrite an existing file only when replacement is explicitly intended. Prefer edit_file for targeted changes to existing files because write_file overwrites the full file content.",
+          "source": {
+            "kind": "native"
+          },
+          "category": "write",
+          "invoked": false
+        }
+      ],
+      "context_window": {
+        "provider": "anthropic",
+        "model": "claude-opus-4-8",
+        "context_window_tokens": 1000000,
+        "input_tokens": 34229,
+        "usage_percent": 3.4229,
+        "count_method": "response_usage_scaled_breakdown",
+        "staleness": "live",
+        "generated_at": "2026-07-01T17:06:30.396938306Z",
+        "event_seq": 106,
+        "breakdown": [
+          {
+            "category": "system_prompt",
+            "tokens": 2559,
+            "usage_percent": 0.2559
+          },
+          {
+            "category": "tools",
+            "tokens": 2935,
+            "usage_percent": 0.2935
+          },
+          {
+            "category": "memory",
+            "tokens": 6238,
+            "usage_percent": 0.6238
+          },
+          {
+            "category": "conversation",
+            "tokens": 22489,
+            "usage_percent": 2.2489
+          },
+          {
+            "category": "other",
+            "tokens": 8,
+            "usage_percent": 0.0008
+          }
+        ],
+        "warnings": []
+      },
+      "state": "running"
+    },
+    "start@1": {
+      "first_event_seq": 18,
+      "prompt": null,
+      "response": null,
+      "completion": {
+        "outcome": "succeeded",
+        "notes": null,
+        "failure_reason": null,
+        "timestamp": "2026-07-01T17:04:29.974598484Z"
+      },
+      "provider_used": null,
+      "diff": null,
+      "script_invocation": null,
+      "script_timing": null,
+      "parallel_results": null,
+      "output": null,
+      "started_at": "2026-07-01T17:04:29.974479623Z",
+      "handler": "start",
+      "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"
+    }
+  }
 }
\ No newline at end of file
diff --git a/stages/001-start@1/status.json b/stages/001-start@1/status.json
new file mode 100644
index 000000000..e41abb263
--- /dev/null
+++ b/stages/001-start@1/status.json
@@ -0,0 +1,6 @@
+{
+  "outcome": "succeeded",
+  "notes": null,
+  "failure_reason": null,
+  "timestamp": "2026-07-01T17:04:29.974598484Z"
+}
\ No newline at end of file
diff --git a/stages/002-patch@1/prompt.md b/stages/002-patch@1/prompt.md
new file mode 100644
index 000000000..aa1b38070
--- /dev/null
+++ b/stages/002-patch@1/prompt.md
@@ -0,0 +1,4 @@
+Goal: Triage GitHub Dependabot alerts and open verified dependency-patch PRs
+
+
+/eng-patch-cves
\ No newline at end of file
diff --git a/stages/002-patch@1/provider_used.json b/stages/002-patch@1/provider_used.json
new file mode 100644
index 000000000..312da937d
--- /dev/null
+++ b/stages/002-patch@1/provider_used.json
@@ -0,0 +1,5 @@
+{
+  "mode": "agent",
+  "provider": "anthropic",
+  "model": "claude-opus-4-8"
+}
\ No newline at end of file
diff --git a/stages/002-patch@1/response.md b/stages/002-patch@1/response.md
new file mode 100644
index 000000000..fa6d50451
--- /dev/null
+++ b/stages/002-patch@1/response.md
@@ -0,0 +1,40 @@
+I've hit a hard blocker and cannot make progress on this task. Here's the precise diagnosis:
+
+## Blocker: no GitHub access + shell is unusable
+
+Every shell invocation — even `echo hello` — fails before executing, with:
+
+```
+failed to mint GitHub installation access token:
+GitHub App does not have access to repository fabro.
+Update the installation's repository permissions to include it.
+```
+
+This is fatal for this specific goal, because "triage Dependabot alerts and open verified patch PRs" depends entirely on things I now can't do:
+
+| Step | Requires | Status |
+|------|----------|--------|
+| List Dependabot alerts | Authenticated GitHub Security API (`security_events: read`) | ❌ no token / no repo access |
+| Create branch, commit, push | `git` via shell + repo write | ❌ shell blocked, no access |
+| Open PRs | GitHub PR API (`pull_requests: write`) | ❌ no access |
+| Verify fixes (`cargo build`, `cargo nextest`) | shell | ❌ shell blocked |
+
+I 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.
+
+## What I did *not* do
+
+I did not fabricate any alerts, branches, or PRs. Nothing was changed.
+
+## What needs to happen to unblock
+
+1. **Grant the GitHub App installation access to the `fabro` repository** (the error message says this directly). The installation needs, at minimum:
+   - `security_events: read` (to read Dependabot alerts)
+   - `contents: write` + `pull_requests: write` (to push branches and open PRs)
+2. **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.
+
+## How would you like to proceed?
+
+- 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.
+- 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.
+
+Which do you prefer?
\ No newline at end of file