checkpoint

⚒️ Generated with [Fabro](https://fabro.sh)

run.json

@@ -376,7 +376,7 @@
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   "status_updated_at": "2026-07-01T21:51:27.582462398Z",
-  "last_event_at": "2026-07-01T21:51:29.167363953Z",
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   "checkpoints": [
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@@ -417,9 +417,9 @@
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+        "timestamp": "2026-07-01T21:51:34.358990597Z",
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@@ -427,12 +427,79 @@
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           "internal.run_id": "01KWFTMDQVT7SD0GRRWKXH776E",
-          "thread.start.current_node": "preflight",
+          "failure_class": "",
           "internal.node_visit_count": 1,
+          "internal.fidelity": "compact",
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+          "command.output": "blob://sha256/ea19cd83eed4d9599888bd0cad534de695ad3b85b6ab2941a381ee0e88808c99",
+          "failure_signature": "",
+          "internal.thread_id": "start",
+          "internal.work_dir": "/home/daytona/workspace/fabro",
+          "internal.retry_count.preflight": 0,
+          "outcome": "succeeded",
+          "thread.start.current_node": "preflight",
           "current_node": "preflight",
+          "graph.max_node_visits": "40",
+          "graph.rankdir": "LR"
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+            },
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+            "usage": null,
+            "timing": {
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+        "git_commit_sha": "d99b47378aa726dffc81c823c92474f1b6e6c87e",
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+          "start": 1
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+      "checkpoint": {
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+        "current_node": "plan",
+        "completed_nodes": [
+          "start",
+          "preflight",
+          "plan"
+        ],
+        "node_retries": {},
+        "context_values": {
+          "response.plan": "Plan written to `merge-train-plan.md`.\n\n**Summary:**\n\n- **READY (2):** Both PRs qualify — open, not draft, target `main`, head branches in `fabro-sh/fabro` (not forks), both `MERGEABLE`.\n  1. **#543** — `feat: grant Dependabot alerts read/write...` (branch `add-dependabot-alerts-app-scope`)\n  2. **#544** — `fix: grant organization_projects...` (branch `add-organization-projects-app-scope`)\n- **SKIP:** none.\n- **Order:** keep requested **543 → 544**. No dependency; independent permission additions.\n- **Conflict warning:** #544 **will conflict** after #543 merges. Both edit the identical `\"emails\": \"read\"` line and insert a test assertion at the same spot in `install.rs` (both cli + server crates). The conflict is additive/trivial — resolution is to **keep both permission keys** (`vulnerability_alerts` and `organization_projects`) and **both test assertions**, fix trailing commas, then verify with `cargo nextest run -p fabro-cli -p fabro-server`.\n\nPlan path: `/home/daytona/workspace/fabro/merge-train-plan.md`",
+          "internal.thread_id": "preflight",
+          "graph.goal": "Merge the pull requests 543,544 into main as a merge train: process them in the given order, rebasing each onto the latest main (so each PR is validated against the cumulative result of the ones before it), resolving conflicts, pushing, and merging with the squash method. Stop at the first PR that cannot be merged cleanly and report why.",
+          "thread.preflight.current_node": "plan",
+          "internal.run_id": "01KWFTMDQVT7SD0GRRWKXH776E",
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           "command.output": "blob://sha256/ea19cd83eed4d9599888bd0cad534de695ad3b85b6ab2941a381ee0e88808c99",
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@@ -442,13 +509,56 @@
           "graph.rankdir": "LR",
           "outcome": "succeeded",
           "graph.max_node_visits": "40",
-          "internal.retry_count.start": 0
+          "internal.retry_count.start": 0,
+          "last_response": "Plan written to `merge-train-plan.md`.\n\n**Summary:**\n\n- **READY (2):** Both PRs qualify — open, not draft, target `main`, head branches in `fabro-sh/fabro` (not forks), both `MERGEABLE`.\n  1. **#543",
+          "last_stage": "plan"
         },
         "node_outcomes": {
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             "status": "succeeded",
             "usage": null
           },
+          "plan": {
+            "status": "succeeded",
+            "context_updates": {
+              "response.plan": "Plan written to `merge-train-plan.md`.\n\n**Summary:**\n\n- **READY (2):** Both PRs qualify — open, not draft, target `main`, head branches in `fabro-sh/fabro` (not forks), both `MERGEABLE`.\n  1. **#543** — `feat: grant Dependabot alerts read/write...` (branch `add-dependabot-alerts-app-scope`)\n  2. **#544** — `fix: grant organization_projects...` (branch `add-organization-projects-app-scope`)\n- **SKIP:** none.\n- **Order:** keep requested **543 → 544**. No dependency; independent permission additions.\n- **Conflict warning:** #544 **will conflict** after #543 merges. Both edit the identical `\"emails\": \"read\"` line and insert a test assertion at the same spot in `install.rs` (both cli + server crates). The conflict is additive/trivial — resolution is to **keep both permission keys** (`vulnerability_alerts` and `organization_projects`) and **both test assertions**, fix trailing commas, then verify with `cargo nextest run -p fabro-cli -p fabro-server`.\n\nPlan path: `/home/daytona/workspace/fabro/merge-train-plan.md`",
+              "last_response": "Plan written to `merge-train-plan.md`.\n\n**Summary:**\n\n- **READY (2):** Both PRs qualify — open, not draft, target `main`, head branches in `fabro-sh/fabro` (not forks), both `MERGEABLE`.\n  1. **#543",
+              "last_stage": "plan"
+            },
+            "notes": "Stage completed: plan",
+            "usage": {
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+                    "model_id": "claude-opus-4-8"
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+                    "output_tokens": 2316,
+                    "reasoning_tokens": 0,
+                    "cache_read_tokens": 53006,
+                    "cache_write_tokens": 15608
+                  }
+                },
+                "facts": {
+                  "algorithm": "anthropic",
+                  "cache_write_5m_tokens": 15608,
+                  "cache_write_1h_tokens": 0
+                }
+              },
+              "total_usd_micros": 205728
+            },
+            "files_touched": [
+              "/home/daytona/workspace/fabro/merge-train-plan.md"
+            ],
+            "timing": {
+              "wall_time_ms": 0,
+              "inference_time_ms": 31587,
+              "tool_time_ms": 2552,
+              "active_time_ms": 34139
+            }
+          },
           "preflight": {
             "status": "succeeded",
             "context_updates": {
@@ -464,10 +574,11 @@
             }
           }
         },
-        "next_node_id": "plan",
+        "next_node_id": "train",
         "node_visits": {
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+          "plan": 1
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       "diff": {}
@@ -533,11 +644,244 @@
       },
       "state": "succeeded"
     },
+    "plan@1": {
+      "first_event_seq": 32,
+      "prompt": null,
+      "response": null,
+      "completion": null,
+      "provider_used": {
+        "mode": "agent",
+        "provider": "anthropic",
+        "model": "claude-opus-4-8",
+        "reasoning_effort": "high"
+      },
+      "diff": null,
+      "script_invocation": null,
+      "script_timing": null,
+      "parallel_results": null,
+      "output": null,
+      "started_at": "2026-07-01T21:51:34.360616040Z",
+      "handler": "agent",
+      "usage": {
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+        "output_tokens": 2316,
+        "total_tokens": 75685,
+        "reasoning_tokens": 0,
+        "cache_read_tokens": 53006,
+        "cache_write_tokens": 15608,
+        "total_usd_micros": 205728
+      },
+      "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": false
+        },
+        {
+          "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": false
+        },
+        {
+          "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": false
+        },
+        {
+          "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": true
+        }
+      ],
+      "context_window": {
+        "provider": "anthropic",
+        "model": "claude-opus-4-8",
+        "context_window_tokens": 1000000,
+        "input_tokens": 16816,
+        "usage_percent": 1.6816,
+        "count_method": "response_usage_scaled_breakdown",
+        "staleness": "live",
+        "generated_at": "2026-07-01T21:52:08.972299983Z",
+        "event_seq": 53,
+        "breakdown": [
+          {
+            "category": "system_prompt",
+            "tokens": 2419,
+            "usage_percent": 0.2419
+          },
+          {
+            "category": "tools",
+            "tokens": 2759,
+            "usage_percent": 0.2759
+          },
+          {
+            "category": "memory",
+            "tokens": 5865,
+            "usage_percent": 0.5865
+          },
+          {
+            "category": "conversation",
+            "tokens": 5763,
+            "usage_percent": 0.5763
+          },
+          {
+            "category": "other",
+            "tokens": 10,
+            "usage_percent": 0.001
+          }
+        ],
+        "warnings": []
+      },
+      "state": "running"
+    },
     "preflight@1": {
       "first_event_seq": 22,
       "prompt": null,
       "response": null,
-      "completion": null,
+      "completion": {
+        "outcome": "succeeded",
+        "notes": "Script completed: gh auth status 2>&1 && git fetch --prune origin 2>&1 && echo 'preflight ok'",
+        "failure_reason": null,
+        "timestamp": "2026-07-01T21:51:31.181094768Z"
+      },
       "provider_used": null,
       "diff": null,
       "script_invocation": {
@@ -545,11 +889,27 @@
         "command": "exec 2>&1\ngh auth status 2>&1 && git fetch --prune origin 2>&1 && echo 'preflight ok'",
         "language": "shell"
       },
-      "script_timing": null,
+      "script_timing": {
+        "output": "blob://sha256/ea19cd83eed4d9599888bd0cad534de695ad3b85b6ab2941a381ee0e88808c99",
+        "exit_code": 0,
+        "duration_ms": 1742,
+        "termination": "exited",
+        "output_bytes": 209,
+        "live_streaming": true
+      },
       "parallel_results": null,
       "output": null,
+      "output_bytes": 209,
+      "live_streaming": true,
+      "termination": "exited",
       "started_at": "2026-07-01T21:51:29.167336080Z",
       "handler": "command",
+      "timing": {
+        "wall_time_ms": 2013,
+        "inference_time_ms": 0,
+        "tool_time_ms": 1742,
+        "active_time_ms": 1742
+      },
       "usage": {
         "input_tokens": 0,
         "output_tokens": 0,
@@ -558,7 +918,7 @@
         "cache_read_tokens": 0,
         "cache_write_tokens": 0
       },
-      "state": "running"
+      "state": "succeeded"
     }
   }
 }

stages/002-preflight@1/output.log

@@ -0,0 +1 @@
+blob://sha256/ea19cd83eed4d9599888bd0cad534de695ad3b85b6ab2941a381ee0e88808c99

stages/002-preflight@1/script_timing.json

@@ -0,0 +1,8 @@
+{
+  "output": "blob://sha256/ea19cd83eed4d9599888bd0cad534de695ad3b85b6ab2941a381ee0e88808c99",
+  "exit_code": 0,
+  "duration_ms": 1742,
+  "termination": "exited",
+  "output_bytes": 209,
+  "live_streaming": true
+}

stages/002-preflight@1/status.json

@@ -0,0 +1,6 @@
+{
+  "outcome": "succeeded",
+  "notes": "Script completed: gh auth status 2>&1 && git fetch --prune origin 2>&1 && echo 'preflight ok'",
+  "failure_reason": null,
+  "timestamp": "2026-07-01T21:51:31.181094768Z"
+}

stages/003-plan@1/prompt.md

@@ -0,0 +1,48 @@
+Goal: Merge the pull requests 543,544 into main as a merge train: process them in the given order, rebasing each onto the latest main (so each PR is validated against the cumulative result of the ones before it), resolving conflicts, pushing, and merging with the squash method. Stop at the first PR that cannot be merged cleanly and report why.
+
+## Completed stages
+- **preflight**: succeeded
+  - Script: `gh auth status 2>&1 && git fetch --prune origin 2>&1 && echo 'preflight ok'`
+  - Output:
+    ```
+    github.com
+      ✓ Logged in to github.com account fabro-sh-fabro[bot] (GITHUB_TOKEN)
+      - Active account: true
+      - Git operations protocol: https
+      - Token: ghs_************************************
+    preflight ok
+    ```
+
+
+You are planning a **merge train**. The ordered, comma-separated list of PR
+numbers to merge is in the goal (input `prs`), targeting the base branch (input
+`base`). You will NOT merge, push, rebase, or change any code in this stage —
+this is analysis only. Produce a plan for the next stage to execute.
+
+## Steps
+
+1. Parse the PR list from the goal, preserving the given order.
+2. For each PR, gather facts with the `gh` CLI, e.g.:
+   `gh pr view <n> --json number,title,state,isDraft,mergeable,baseRefName,headRefName,headRepositoryOwner,author,url`
+3. Classify each PR into exactly one bucket:
+   - **READY** — open, not draft, targets the base branch, and its head branch is
+     in THIS repository (not a fork). Only READY PRs are eligible to be merged.
+   - **SKIP** — closed/already merged, draft, targets a different base, or its head
+     is on a **fork** (we cannot push conflict fixes to a fork's branch, so the
+     train can't rebase it). Record the specific reason.
+4. Decide the final merge order. Default to the given order. If you can tell from
+   the diffs that one PR logically depends on another, note it, but do not
+   silently reorder — call out any ordering concern for a human to confirm.
+5. Flag likely conflicts: if two READY PRs touch the same files/regions, note that
+   the later one will almost certainly need conflict resolution once the earlier
+   one merges (this is expected and the train will handle it).
+
+## Output
+
+Write `merge-train-plan.md` containing:
+- The ordered list of READY PRs (number, title, head branch) to merge.
+- The SKIP list with a one-line reason each.
+- Any ordering or conflict warnings.
+
+Then respond with a short summary and the path to the plan file. If there are
+zero READY PRs, say so plainly — the train stage will simply report nothing to do.

stages/003-plan@1/provider_used.json

@@ -0,0 +1,6 @@
+{
+  "mode": "agent",
+  "provider": "anthropic",
+  "model": "claude-opus-4-8",
+  "reasoning_effort": "high"
+}

stages/003-plan@1/response.md

@@ -0,0 +1,12 @@
+Plan written to `merge-train-plan.md`.
+
+**Summary:**
+
+- **READY (2):** Both PRs qualify — open, not draft, target `main`, head branches in `fabro-sh/fabro` (not forks), both `MERGEABLE`.
+  1. **#543** — `feat: grant Dependabot alerts read/write...` (branch `add-dependabot-alerts-app-scope`)
+  2. **#544** — `fix: grant organization_projects...` (branch `add-organization-projects-app-scope`)
+- **SKIP:** none.
+- **Order:** keep requested **543 → 544**. No dependency; independent permission additions.
+- **Conflict warning:** #544 **will conflict** after #543 merges. Both edit the identical `"emails": "read"` line and insert a test assertion at the same spot in `install.rs` (both cli + server crates). The conflict is additive/trivial — resolution is to **keep both permission keys** (`vulnerability_alerts` and `organization_projects`) and **both test assertions**, fix trailing commas, then verify with `cargo nextest run -p fabro-cli -p fabro-server`.
+
+Plan path: `/home/daytona/workspace/fabro/merge-train-plan.md`