diff --git a/entry b/entry
index 2e2104d..9b4a0ac 100755
--- a/entry
+++ b/entry
@@ -141043,7 +141043,9 @@ async function checkoutPrBranch(pullNumber, params) {
     log.debug(`already on PR branch ${localBranch}, skipping checkout`);
   } else {
     log.debug(`\xBB fetching base branch (${baseBranch})...`);
-    $git("fetch", ["--no-tags", "origin", baseBranch], {
+    const isShallow = $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim();
+    const baseFetchArgs = isShallow === "true" ? ["--deepen=1000", "--no-tags", "origin", baseBranch] : ["--no-tags", "origin", baseBranch];
+    $git("fetch", baseFetchArgs, {
       token: gitToken,
       restricted: shell !== "enabled"
     });
@@ -141058,7 +141060,9 @@ async function checkoutPrBranch(pullNumber, params) {
   }
   if (alreadyOnBranch) {
     log.debug(`\xBB fetching base branch (${baseBranch})...`);
-    $git("fetch", ["--no-tags", "origin", baseBranch], {
+    const isShallow = $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim();
+    const baseFetchArgs = isShallow === "true" ? ["--deepen=1000", "--no-tags", "origin", baseBranch] : ["--no-tags", "origin", baseBranch];
+    $git("fetch", baseFetchArgs, {
       token: gitToken,
       restricted: shell !== "enabled"
     });
@@ -143145,7 +143149,7 @@ var SetOutputParams = type({
 function SetOutputTool(ctx) {
   return tool({
     name: "set_output",
-    description: "Set the action output. When called by a subagent, returns a summary result to the orchestrator. When called in standalone mode, exposes the value as the 'result' GitHub Action output.",
+    description: "Set the action output. When called by a subagent, returns a summary result to the orchestrator \u2014 this is the ONLY way to pass results back. When called by the orchestrator in standalone mode (trigger: unknown), exposes the value as the 'result' GitHub Action output for downstream workflow steps. Do NOT use this for progress reporting \u2014 use report_progress instead.",
     parameters: SetOutputParams,
     execute: execute(async (params) => {
       const selfId = ctx.toolState.selfSubagentId;
@@ -147359,8 +147363,6 @@ To investigate questions, prefer \`${ghPullfrogMcpName}/ask_question\` over \`${
 
 After each \`delegate\` call, you receive a \`results\` array \u2014 one entry per task with \`label\`, \`success\`, \`summary\` (from set_output), and \`stdoutFile\` (inspectable via \`${ghPullfrogMcpName}/file_read\`). Follow the post-delegation steps from the select_mode guidance.
 
-When all delegations are complete, call \`${ghPullfrogMcpName}/set_output\` with the final result. This makes it available as the GitHub Action output.
-
 ### Subagent capabilities
 
 Subagents have: file operations, shell (for local git, tests, builds), read-only GitHub queries, and upload_file. They do NOT have: \`git\`, \`checkout_pr\`, \`push_branch\`, \`create_pull_request\`, \`create_pull_request_review\`, \`report_progress\`, \`create_issue_comment\`, \`reply_to_review_comment\`, \`resolve_review_thread\`, \`delegate\`, \`ask_question\`, or any dependency/remote-mutating tools. All GitHub-write and state-mutating operations are your responsibility.
diff --git a/mcp/checkout.ts b/mcp/checkout.ts
index ac0c864..2237a23 100644
--- a/mcp/checkout.ts
+++ b/mcp/checkout.ts
@@ -214,9 +214,17 @@ export async function checkoutPrBranch(
   if (alreadyOnBranch) {
     log.debug(`already on PR branch ${localBranch}, skipping checkout`);
   } else {
-    // fetch base branch so origin/<base> exists for diff operations
+    // fetch base branch so origin/<base> exists for diff operations.
+    // deepen if shallow — actions/checkout uses depth=1 by default, which
+    // breaks rebase/log operations because git can't find the merge base
+    // between the shallow base and the fully-fetched PR branch.
     log.debug(`» fetching base branch (${baseBranch})...`);
-    $git("fetch", ["--no-tags", "origin", baseBranch], {
+    const isShallow = $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim();
+    const baseFetchArgs =
+      isShallow === "true"
+        ? ["--deepen=1000", "--no-tags", "origin", baseBranch]
+        : ["--no-tags", "origin", baseBranch];
+    $git("fetch", baseFetchArgs, {
       token: gitToken,
       restricted: shell !== "enabled",
     });
@@ -241,7 +249,12 @@ export async function checkoutPrBranch(
   // fetch if we skipped checkout (already on branch) - otherwise already fetched above
   if (alreadyOnBranch) {
     log.debug(`» fetching base branch (${baseBranch})...`);
-    $git("fetch", ["--no-tags", "origin", baseBranch], {
+    const isShallow = $("git", ["rev-parse", "--is-shallow-repository"], { log: false }).trim();
+    const baseFetchArgs =
+      isShallow === "true"
+        ? ["--deepen=1000", "--no-tags", "origin", baseBranch]
+        : ["--no-tags", "origin", baseBranch];
+    $git("fetch", baseFetchArgs, {
       token: gitToken,
       restricted: shell !== "enabled",
     });
diff --git a/mcp/output.ts b/mcp/output.ts
index 0e25bb4..8a3704a 100644
--- a/mcp/output.ts
+++ b/mcp/output.ts
@@ -11,7 +11,7 @@ export function SetOutputTool(ctx: ToolContext) {
   return tool({
     name: "set_output",
     description:
-      "Set the action output. When called by a subagent, returns a summary result to the orchestrator. When called in standalone mode, exposes the value as the 'result' GitHub Action output.",
+      "Set the action output. When called by a subagent, returns a summary result to the orchestrator — this is the ONLY way to pass results back. When called by the orchestrator in standalone mode (trigger: unknown), exposes the value as the 'result' GitHub Action output for downstream workflow steps. Do NOT use this for progress reporting — use report_progress instead.",
     parameters: SetOutputParams,
     execute: execute(async (params) => {
       const selfId = ctx.toolState.selfSubagentId;
diff --git a/test/agnostic/delegate.ts b/test/agnostic/delegate.ts
index 3c9070c..068a273 100644
--- a/test/agnostic/delegate.ts
+++ b/test/agnostic/delegate.ts
@@ -12,7 +12,9 @@ import { defineFixture, getAgentOutput, getStructuredOutput } from "../utils.ts"
 const fixture = defineFixture(
   {
     prompt: `Select the Plan mode via select_mode, then delegate with mini effort. Your subagent instructions should be:
-"This is a delegation test. Your only task is to call set_output with the value 'DELEGATE_BASIC_PASSED'. Do not create plans, branches, or PRs. Just call set_output."`,
+"This is a delegation test. Your only task is to call set_output with the value 'DELEGATE_BASIC_PASSED'. Do not create plans, branches, or PRs. Just call set_output."
+
+When all delegations are complete, call set_output with the final result. This makes it available as the GitHub Action output.`,
     effort: "mini",
     timeout: "5m",
   },
diff --git a/test/agnostic/delegateEffort.ts b/test/agnostic/delegateEffort.ts
index 03dcd61..1241eda 100644
--- a/test/agnostic/delegateEffort.ts
+++ b/test/agnostic/delegateEffort.ts
@@ -16,7 +16,9 @@ const fixture = defineFixture(
   {
     prompt: `This is a simple task. Select the Plan mode via select_mode, then delegate with MINI effort (this is a trivial task).
 Your subagent instructions should be:
-"Call set_output with the value 'EFFORT_TEST_PASSED'. Do not create plans or PRs. Just call set_output."`,
+"Call set_output with the value 'EFFORT_TEST_PASSED'. Do not create plans or PRs. Just call set_output."
+
+When all delegations are complete, call set_output with the final result. This makes it available as the GitHub Action output.`,
     effort: "auto",
     timeout: "5m",
   },
diff --git a/test/agnostic/delegateMulti.ts b/test/agnostic/delegateMulti.ts
index 35023de..3920a71 100644
--- a/test/agnostic/delegateMulti.ts
+++ b/test/agnostic/delegateMulti.ts
@@ -19,7 +19,9 @@ Phase 1: Select Plan mode via select_mode, then delegate with tasks: [{ label: "
 
 Phase 2: After Phase 1 completes, select Plan mode again and delegate with tasks: [{ label: "phase-2", instructions: "Your task is to call set_output with the value 'MULTI_DELEGATE_PASSED'. Do not create plans or PRs.", effort: "mini" }]. Include the result from Phase 1 in the instructions if you want.
 
-Both delegations must complete successfully.`,
+Both delegations must complete successfully.
+
+When all delegations are complete, call set_output with the final result. This makes it available as the GitHub Action output.`,
     effort: "mini",
     timeout: "8m",
   },
diff --git a/utils/instructions.ts b/utils/instructions.ts
index efbbdda..f7bc99c 100644
--- a/utils/instructions.ts
+++ b/utils/instructions.ts
@@ -384,8 +384,6 @@ To investigate questions, prefer \`${ghPullfrogMcpName}/ask_question\` over \`${
 
 After each \`delegate\` call, you receive a \`results\` array — one entry per task with \`label\`, \`success\`, \`summary\` (from set_output), and \`stdoutFile\` (inspectable via \`${ghPullfrogMcpName}/file_read\`). Follow the post-delegation steps from the select_mode guidance.
 
-When all delegations are complete, call \`${ghPullfrogMcpName}/set_output\` with the final result. This makes it available as the GitHub Action output.
-
 ### Subagent capabilities
 
 Subagents have: file operations, shell (for local git, tests, builds), read-only GitHub queries, and upload_file. They do NOT have: \`git\`, \`checkout_pr\`, \`push_branch\`, \`create_pull_request\`, \`create_pull_request_review\`, \`report_progress\`, \`create_issue_comment\`, \`reply_to_review_comment\`, \`resolve_review_thread\`, \`delegate\`, \`ask_question\`, or any dependency/remote-mutating tools. All GitHub-write and state-mutating operations are your responsibility.