🔧 Fetch origin before mission dispatch and enforce rebase-only policy

MISSION.md

@@ -56,11 +56,12 @@ You are working on GitHub issue `{{ issue.identifier }}`: {{ issue.title }}
 You are working in a git worktree on branch `mission/{{ issue.identifier | downcase }}`.
 
 1. **Read project guidelines** — check for AGENTS.md, CLAUDE.md, or similar files first.
-2. **Post your workpad** — use your mission tools to post a plan on the issue before writing code.
-3. **Understand the codebase** — explore the relevant code before making changes.
-4. **Implement** — make focused, minimal changes. Run tests and linters.
-5. **Commit** — keep commits clean and atomic. Update your workpad as you go.
-6. **Create a PR** targeting `main` when complete. Attach it to the issue.
+2. **Sync with latest `main`** — before writing code, fetch the latest changes and rebase your worktree branch onto `origin/main` (or the configured base branch). Prefer `git pull --rebase` / `git fetch` + `git rebase`. Do not create merge commits.
+3. **Post your workpad** — use your mission tools to post a plan on the issue before writing code.
+4. **Understand the codebase** — explore the relevant code before making changes.
+5. **Implement** — make focused, minimal changes. Run tests and linters.
+6. **Commit** — keep commits clean and atomic. Update your workpad as you go.
+7. **Create a PR** targeting `main` when complete. Attach it to the issue.
 
 ## Rules
 
@@ -69,4 +70,6 @@ You are working in a git worktree on branch `mission/{{ issue.identifier | downc
 - Do not expand scope. File follow-up issues for anything tangential.
 - Keep the workpad updated — it is the primary way humans track your progress.
 - Use gitmoji in commit messages and PR titles (e.g. ✨, 🐛, ♻️, 🔧).
+- Prefer rebases over merges when syncing with the base branch.
+- **NEVER create merge commits.** Keep mission branches linear.
 - **NEVER merge PRs.** Create the PR, verify CI passes, and address any review feedback — but leave merging to a human.

orbitdock-server/crates/connector-claude/src/lib.rs

@@ -589,9 +589,25 @@ impl ClaudeConnector {
         if allow_bypass_permissions {
             args.push("--allow-dangerously-skip-permissions");
         }
-        let allowed_joined = allowed_tools.join(",");
+
+        // When permission_mode is "acceptEdits", ensure edit tools are explicitly
+        // in the allowedTools list. The --permission-prompt-tool stdio flag routes
+        // ALL permission decisions through the control protocol, so the CLI's
+        // internal --permission-mode auto-accept logic may not fire. Passing them
+        // as --allowedTools guarantees the CLI pre-approves them.
+        let mut effective_allowed: Vec<String> = allowed_tools.to_vec();
+        if permission_mode == Some("acceptEdits") {
+            for tool in ["Edit", "Write", "NotebookEdit"] {
+                let tool_str = tool.to_string();
+                if !effective_allowed.contains(&tool_str) {
+                    effective_allowed.push(tool_str);
+                }
+            }
+        }
+
+        let allowed_joined = effective_allowed.join(",");
         let disallowed_joined = disallowed_tools.join(",");
-        if !allowed_tools.is_empty() {
+        if !effective_allowed.is_empty() {
             args.extend(["--allowedTools", &allowed_joined]);
         }
         if !disallowed_tools.is_empty() {

orbitdock-server/crates/server/src/domain/git/repo.rs

@@ -257,6 +257,11 @@ pub async fn delete_remote_branch(repo_path: &str, branch: &str) -> Result<(), S
     run_git_checked(&["push", "origin", "--delete", branch], repo_path).await
 }
 
+/// Fetch the latest refs from `origin`.
+pub async fn fetch_origin(repo_path: &str) -> Result<(), String> {
+    run_git_checked(&["fetch", "origin"], repo_path).await
+}
+
 /// Initialize a new git repository at the given path.
 pub async fn git_init(path: &str) -> Result<(), String> {
     run_git_checked(&["init"], path).await

orbitdock-server/crates/server/src/domain/instructions.rs

@@ -123,6 +123,17 @@ multiple comments. One living document.
 - Use `mission_report_blocked` only for true blockers (missing auth, secrets, permissions)
 - Create a PR when complete, then use `mission_link_pr` to attach it to the issue
 - **NEVER merge PRs.** After opening the PR, check CI status and address review feedback — but leave merging to a human.
-- If you discover out-of-scope work, use `mission_create_followup` instead of expanding scope"#
+- If you discover out-of-scope work, use `mission_create_followup` instead of expanding scope
+
+## Git Workflow
+
+Your worktree is automatically based on the latest remote base branch at dispatch time.
+Keep your branch linear — **never create merge commits**.
+
+- Sync with base branch: `git fetch origin && git rebase origin/main` (or the configured base branch)
+- Prefer `git pull --rebase` over `git pull`
+- If you need to stay current mid-work: `git fetch origin && git rebase origin/main`
+- **NEVER** run `git merge` — always rebase
+- Keep commits clean and atomic"#
         .to_string()
 }

orbitdock-server/crates/server/src/domain/mission_control/template.rs

@@ -82,18 +82,22 @@ You are working on {issue_label} `{{{{ issue.identifier }}}}`: {{{{ issue.title
 You are working in a git worktree on branch `mission/{{{{ issue.identifier | downcase }}}}`.
 
 1. **Read project guidelines** — check for AGENTS.md, CLAUDE.md, or similar files first.
-2. **Post your workpad** — use your mission tools to post a plan on the issue before writing code.
-3. **Understand the codebase** — explore the relevant code before making changes.
-4. **Implement** — make focused, minimal changes. Run tests and linters.
-5. **Commit** — keep commits clean and atomic. Update your workpad as you go.
-6. **Create a PR** targeting `main` when complete. Attach it to the issue.
+2. **Sync with latest `main`** — before writing code, fetch the latest changes and rebase your worktree branch onto `origin/main` (or the configured base branch). Prefer `git pull --rebase` / `git fetch` + `git rebase`. Do not create merge commits.
+3. **Post your workpad** — use your mission tools to post a plan on the issue before writing code.
+4. **Understand the codebase** — explore the relevant code before making changes.
+5. **Implement** — make focused, minimal changes. Run tests and linters.
+6. **Commit** — keep commits clean and atomic. Update your workpad as you go.
+7. **Create a PR** targeting `main` when complete. Attach it to the issue.
 
 ## Rules
 
 - Work autonomously end-to-end. Do not ask for human follow-up.
 - Stop early only for true blockers (missing auth, permissions, secrets).
 - Do not expand scope. File follow-up issues for anything tangential.
 - Keep the workpad updated — it is the primary way humans track your progress.
+- Prefer rebases over merges when syncing with the base branch.
+- **NEVER create merge commits.** Keep mission branches linear.
+- **NEVER merge PRs.** Create the PR, verify CI passes, and address any review feedback — but leave merging to a human.
 "#
     )
 }

orbitdock-server/crates/server/src/runtime/mission_dispatch.rs

@@ -89,12 +89,27 @@ pub async fn dispatch_issue(
         );
     }
 
+    // Fetch latest refs so the worktree starts from the current remote HEAD
+    if let Err(err) = crate::domain::git::repo::fetch_origin(&ctx.repo_root).await {
+        warn!(
+            component = "mission_control",
+            event = "dispatch.fetch_failed",
+            mission_id = %mission_id,
+            issue_id = %issue.id,
+            error = %err,
+            "git fetch origin failed — worktree will use local state"
+        );
+    }
+
+    // Use origin/<base_branch> so the worktree is based on the freshly-fetched remote ref
+    let remote_base = format!("origin/{}", ctx.base_branch);
+
     // Create worktree via the runtime helper (also persists the record)
     let worktree_path = match crate::runtime::worktree_creation::create_tracked_worktree(
         registry,
         &ctx.repo_root,
         &branch_name,
-        Some(&ctx.base_branch),
+        Some(&remote_base),
         orbitdock_protocol::WorktreeOrigin::Agent,
         ctx.worktree_root_dir.as_deref(),
         true, // always clean up stale worktrees — if we're dispatching, no active session owns them