feat(FN-4068): add branch conflict detection and recovery for stale worktre

Implements branch conflict detection and recovery across the Fusion engine, CLI, and dashboard — surfacing git worktree conflicts when tasks conflict with unrelated branch state, and providing a recovery workflow to resolve them. The executor and worktree pool now integrate typed branch conflict che

Fusion-Task-Id: FN-4068

packages/dashboard/app/components/ResearchView.css

@@ -4,6 +4,7 @@
   gap: var(--space-md);
   height: 100%;
   min-height: 0;
+  overflow: hidden;
   padding: var(--space-lg);
   padding-bottom: var(--space-lg);
 }
@@ -30,6 +31,7 @@
   gap: var(--space-md);
   min-height: 0;
   flex: 1;
+  overflow: hidden;
 }
 
 .research-view__sidebar,
@@ -39,6 +41,26 @@
   flex-direction: column;
   gap: var(--space-md);
   min-height: 0;
+  overflow: hidden;
+}
+
+.research-view__reader {
+  overflow: auto;
+}
+
+.research-view__reader-content {
+  display: flex;
+  flex: 1;
+  flex-direction: column;
+  gap: var(--space-md);
+  min-height: 0;
+}
+
+.research-view__run-detail {
+  display: flex;
+  flex-direction: column;
+  gap: var(--space-md);
+  min-height: 0;
 }
 
 .research-view__form {
@@ -127,6 +149,7 @@
 .research-view__actions {
   display: flex;
   flex-wrap: wrap;
+  align-items: center;
   gap: var(--space-xs);
   margin-top: var(--space-sm);
 }
@@ -171,11 +194,13 @@
   padding-left: var(--space-lg);
 }
 
-
 .research-view__stats {
   display: grid;
   grid-template-columns: repeat(3, minmax(0, 1fr));
   gap: var(--space-sm);
+  margin-top: auto;
+  padding-top: var(--space-sm);
+  border-top: var(--btn-border-width) solid var(--border);
 }
 
 .research-view__stat-card {
@@ -201,6 +226,7 @@
 @media (max-width: 768px) {
   .research-view {
     overflow-y: auto;
+    overflow-x: hidden;
     -webkit-overflow-scrolling: touch;
     padding: var(--space-md);
     padding-bottom: calc(var(--space-md) + var(--mobile-nav-height) + env(safe-area-inset-bottom, 0px) + var(--standalone-bottom-gap));
@@ -210,6 +236,21 @@
     display: flex;
     flex-direction: column;
     grid-template-columns: minmax(0, 1fr);
+    gap: var(--space-md);
+    flex: initial;
+    overflow: visible;
+  }
+
+  .research-view__sidebar,
+  .research-view__reader {
+    overflow: visible;
+  }
+
+  .research-view__reader {
+    overflow: visible;
+  }
+
+  .research-view__reader-content {
     flex: initial;
   }
 
@@ -223,6 +264,10 @@
     flex-direction: column;
   }
 
+  .research-view__header .btn {
+    align-self: flex-start;
+  }
+
   .research-view__stats {
     grid-template-columns: minmax(0, 1fr);
   }

packages/dashboard/app/components/ResearchView.tsx

@@ -322,113 +322,115 @@ export function ResearchView({ projectId, addToast, onOpenSettings, readinessVer
           {loading && <p data-testid="research-state-loading">Loading research runs…</p>}
           {!loading && error && <p data-testid="research-state-error">{error}</p>}
           {!loading && !error && runs.length === 0 && <p data-testid="research-state-empty">No research runs yet</p>}
-          {selectedRun && (
-            <div>
-              <div className="research-view__status-row">
-                <span className={statusDotClass} />
-                <strong>{statusLabel}</strong>
-              </div>
-              <h3 className="research-view__run-title">{selectedRun.title}</h3>
-              <p className="research-view__run-query">{selectedRun.query}</p>
-              <p className="research-view__run-summary" data-testid="research-state-results">{selectedRun.results?.summary ?? "No summary yet."}</p>
-              <div className="research-view__actions">
-                <button
-                  className="btn"
-                  type="button"
-                  title={!runActionState.cancelable ? runActionState.blockingReason : undefined}
-                  disabled={actionLoading === "cancel" || actionLoading === "retry" || !runActionState.cancelable}
-                  onClick={() => void runAction("cancel", () => cancelRun(selectedRun.id), "Run cancelled")}
-                >
-                  Cancel
-                </button>
-                <button
-                  className="btn"
-                  type="button"
-                  title={!runActionState.retryable ? runActionState.blockingReason : undefined}
-                  disabled={actionLoading === "cancel" || actionLoading === "retry" || !runActionState.retryable}
-                  onClick={() => void runAction("retry", () => retryRun(selectedRun.id), "Run retried")}
-                >
-                  Retry
-                </button>
-                {supportedExportFormats.includes("markdown") && <button className="btn" type="button" disabled={actionLoading === "export-markdown"} onClick={() => void handleExport("markdown")}>Export MD</button>}
-                {supportedExportFormats.includes("json") && <button className="btn" type="button" disabled={actionLoading === "export-json"} onClick={() => void handleExport("json")}>Export JSON</button>}
-                {supportedExportFormats.includes("html") && <button className="btn" type="button" disabled={actionLoading === "export-html"} onClick={() => void handleExport("html")}>Export HTML</button>}
-              </div>
-              {selectedRun.error && <p className="research-view__error">{selectedRun.error}</p>}
-              {uiError && (
-                <div className="form-error" role="alert">
-                  <p>{uiError.message}</p>
-                  {uiError.setupHint && <p>{uiError.setupHint}</p>}
-                  {uiError.code === "MISSING_CREDENTIALS" && (
-                    <button className="btn btn-sm" type="button" onClick={() => onOpenSettings?.("authentication")}>
-                      Open Authentication Settings
-                    </button>
-                  )}
-                  {uiError.code === "FEATURE_DISABLED" && (
-                    <button className="btn btn-sm" type="button" onClick={() => onOpenSettings?.("research-project")}>
-                      Open Research Settings
-                    </button>
-                  )}
+          <div className="research-view__reader-content">
+            {selectedRun && (
+              <div className="research-view__run-detail">
+                <div className="research-view__status-row">
+                  <span className={statusDotClass} />
+                  <strong>{statusLabel}</strong>
                 </div>
-              )}
-              {runActionState.blockingReason && (
-                <p className="research-view__run-query">{runActionState.blockingReason}</p>
-              )}
-              {Array.isArray(selectedRun.results?.findings) && selectedRun.results.findings.length > 0 && (
-                <div className="research-view__findings">
-                  {selectedRun.results.findings.map((finding, index) => {
-                    const findingRecord = finding as { id?: string };
-                    const findingId = findingRecord.id?.trim() || `finding-${index + 1}`;
-                    return (
-                      <article key={findingId} className="research-view__finding card">
-                        <h4>{finding.heading}</h4>
-                        <p>{finding.content}</p>
-                        <div className="research-view__actions research-view__finding-actions">
-                          <button
-                            className="btn btn-primary btn-sm"
-                            type="button"
-                            onClick={() => setModalState({ mode: "create", findingId })}
-                          >
-                            Create Task
-                          </button>
-                          <button
-                            className="btn btn-sm"
-                            type="button"
-                            onClick={() => setModalState({ mode: "enrich", findingId })}
-                          >
-                            Enrich Task
-                          </button>
-                        </div>
-                      </article>
-                    );
-                  })}
+                <h3 className="research-view__run-title">{selectedRun.title}</h3>
+                <p className="research-view__run-query">{selectedRun.query}</p>
+                <p className="research-view__run-summary" data-testid="research-state-results">{selectedRun.results?.summary ?? "No summary yet."}</p>
+                <div className="research-view__actions">
+                  <button
+                    className="btn"
+                    type="button"
+                    title={!runActionState.cancelable ? runActionState.blockingReason : undefined}
+                    disabled={actionLoading === "cancel" || actionLoading === "retry" || !runActionState.cancelable}
+                    onClick={() => void runAction("cancel", () => cancelRun(selectedRun.id), "Run cancelled")}
+                  >
+                    Cancel
+                  </button>
+                  <button
+                    className="btn"
+                    type="button"
+                    title={!runActionState.retryable ? runActionState.blockingReason : undefined}
+                    disabled={actionLoading === "cancel" || actionLoading === "retry" || !runActionState.retryable}
+                    onClick={() => void runAction("retry", () => retryRun(selectedRun.id), "Run retried")}
+                  >
+                    Retry
+                  </button>
+                  {supportedExportFormats.includes("markdown") && <button className="btn" type="button" disabled={actionLoading === "export-markdown"} onClick={() => void handleExport("markdown")}>Export MD</button>}
+                  {supportedExportFormats.includes("json") && <button className="btn" type="button" disabled={actionLoading === "export-json"} onClick={() => void handleExport("json")}>Export JSON</button>}
+                  {supportedExportFormats.includes("html") && <button className="btn" type="button" disabled={actionLoading === "export-html"} onClick={() => void handleExport("html")}>Export HTML</button>}
                 </div>
-              )}
-              {Array.isArray(selectedRun.results?.citations) && selectedRun.results!.citations!.length > 0 && (
-                <ul className="research-view__citations">
-                  {selectedRun.results!.citations!.map((citation) => (
-                    <li key={citation}><a href={citation} target="_blank" rel="noreferrer">{citation}</a></li>
-                  ))}
-                </ul>
-              )}
-              {selectedRun.events.length > 0 && (
-                <details>
-                  <summary>Run history</summary>
-                  <ul className="research-view__events">
-                    {selectedRun.events.map((event) => (
-                      <li key={event.id}>{event.message}</li>
+                {selectedRun.error && <p className="research-view__error">{selectedRun.error}</p>}
+                {uiError && (
+                  <div className="form-error" role="alert">
+                    <p>{uiError.message}</p>
+                    {uiError.setupHint && <p>{uiError.setupHint}</p>}
+                    {uiError.code === "MISSING_CREDENTIALS" && (
+                      <button className="btn btn-sm" type="button" onClick={() => onOpenSettings?.("authentication")}>
+                        Open Authentication Settings
+                      </button>
+                    )}
+                    {uiError.code === "FEATURE_DISABLED" && (
+                      <button className="btn btn-sm" type="button" onClick={() => onOpenSettings?.("research-project")}>
+                        Open Research Settings
+                      </button>
+                    )}
+                  </div>
+                )}
+                {runActionState.blockingReason && (
+                  <p className="research-view__run-query">{runActionState.blockingReason}</p>
+                )}
+                {Array.isArray(selectedRun.results?.findings) && selectedRun.results.findings.length > 0 && (
+                  <div className="research-view__findings">
+                    {selectedRun.results.findings.map((finding, index) => {
+                      const findingRecord = finding as { id?: string };
+                      const findingId = findingRecord.id?.trim() || `finding-${index + 1}`;
+                      return (
+                        <article key={findingId} className="research-view__finding card">
+                          <h4>{finding.heading}</h4>
+                          <p>{finding.content}</p>
+                          <div className="research-view__actions research-view__finding-actions">
+                            <button
+                              className="btn btn-primary btn-sm"
+                              type="button"
+                              onClick={() => setModalState({ mode: "create", findingId })}
+                            >
+                              Create Task
+                            </button>
+                            <button
+                              className="btn btn-sm"
+                              type="button"
+                              onClick={() => setModalState({ mode: "enrich", findingId })}
+                            >
+                              Enrich Task
+                            </button>
+                          </div>
+                        </article>
+                      );
+                    })}
+                  </div>
+                )}
+                {Array.isArray(selectedRun.results?.citations) && selectedRun.results!.citations!.length > 0 && (
+                  <ul className="research-view__citations">
+                    {selectedRun.results!.citations!.map((citation) => (
+                      <li key={citation}><a href={citation} target="_blank" rel="noreferrer">{citation}</a></li>
                     ))}
                   </ul>
-                </details>
-              )}
-            </div>
-          )}
-          {!selectedRun && runs.length > 0 && <p>Select a run to view details.</p>}
+                )}
+                {selectedRun.events.length > 0 && (
+                  <details>
+                    <summary>Run history</summary>
+                    <ul className="research-view__events">
+                      {selectedRun.events.map((event) => (
+                        <li key={event.id}>{event.message}</li>
+                      ))}
+                    </ul>
+                  </details>
+                )}
+              </div>
+            )}
+            {!selectedRun && runs.length > 0 && <p>Select a run to view details.</p>}
 
-          <div className="research-view__stats">
-            <div className="research-view__stat-card"><div className="research-view__stat-label">Running</div><div className="research-view__stat-value">{statusCounts.running}</div></div>
-            <div className="research-view__stat-card"><div className="research-view__stat-label">Completed</div><div className="research-view__stat-value">{statusCounts.completed}</div></div>
-            <div className="research-view__stat-card"><div className="research-view__stat-label">Failed</div><div className="research-view__stat-value">{statusCounts.failed}</div></div>
+            <div className="research-view__stats">
+              <div className="research-view__stat-card"><div className="research-view__stat-label">Running</div><div className="research-view__stat-value">{statusCounts.running}</div></div>
+              <div className="research-view__stat-card"><div className="research-view__stat-label">Completed</div><div className="research-view__stat-value">{statusCounts.completed}</div></div>
+              <div className="research-view__stat-card"><div className="research-view__stat-label">Failed</div><div className="research-view__stat-value">{statusCounts.failed}</div></div>
+            </div>
           </div>
         </div>
       </div>

packages/dashboard/app/components/SettingsModal.tsx

@@ -394,6 +394,7 @@ export function SettingsModal({
     autoMerge: true,
     mergeStrategy: "direct",
     recycleWorktrees: false,
+    executorAllowSiblingBranchRename: false,
     worktreeNaming: "random",
     includeTaskIdInCommit: true,
     worktreeInitCommand: "",
@@ -3485,6 +3486,22 @@ export function SettingsModal({
               </label>
               <small>When enabled, completed task worktrees are returned to an idle pool instead of being deleted, preserving build caches for faster startup</small>
             </div>
+            <div className="form-group">
+              <label htmlFor="executorAllowSiblingBranchRename" className="checkbox-label">
+                <input
+                  id="executorAllowSiblingBranchRename"
+                  type="checkbox"
+                  checked={form.executorAllowSiblingBranchRename === true}
+                  onChange={(e) =>
+                    setForm((f) => ({ ...f, executorAllowSiblingBranchRename: e.target.checked }))
+                  }
+                />
+                Allow silent sibling branch rename during executor conflicts
+              </label>
+              <small>
+                Discouraged. This restores the legacy behavior where a live <code>fusion/&lt;task-id&gt;</code> branch collision silently forks work onto sibling branches like <code>-2</code> and can hide prior commits from the default recovery flow.
+              </small>
+            </div>
             <div className="form-group">
               <label htmlFor="worktreeNaming">Worktree Naming Style</label>
               <select

packages/dashboard/app/components/__tests__/ResearchView.test.tsx

@@ -525,12 +525,27 @@ describe("ResearchView", () => {
     await waitFor(() => expect(enrichButton).not.toBeDisabled());
   });
 
-  it("FN-3912: research view content is scrollable on mobile", () => {
-    const css = loadAllAppCss();
+  it("FN-3912: keeps the desktop research split view as a bounded grid", () => {
     const baseCss = loadAllAppCssBaseOnly();
 
-    expect(baseCss).toMatch(/\.research-view__layout\s*\{[^}]*display:\s*grid;[^}]*grid-template-columns:\s*minmax\(0,\s*1fr\)\s*minmax\(0,\s*2fr\);[^}]*\}/);
+    expect(baseCss).toMatch(/\.research-view__layout\s*\{[^}]*display:\s*grid;[^}]*grid-template-columns:\s*minmax\(0,\s*1fr\)\s*minmax\(0,\s*2fr\);[^}]*overflow:\s*hidden;[^}]*\}/);
+    expect(baseCss).toMatch(/\.research-view__stats\s*\{[^}]*margin-top:\s*auto;[^}]*border-top:\s*var\(--btn-border-width\)\s+solid\s+var\(--border\);[^}]*\}/);
+    expect(baseCss).not.toMatch(/\.research-view__stats\s*\{[^}]*position:\s*absolute;[^}]*\}/);
+  });
 
-    expect(css).toMatch(/@media\s*\(max-width:\s*768px\)\s*\{[^}]*\.research-view\s*\{[^}]*overflow-y:\s*auto;[^}]*-webkit-overflow-scrolling:\s*touch;[^}]*padding-bottom:\s*calc\(var\(--space-md\)\s*\+\s*var\(--mobile-nav-height\)\s*\+\s*env\(safe-area-inset-bottom,\s*0px\)\s*\+\s*var\(--standalone-bottom-gap\)\);[^}]*\}/);
+  it("FN-3912: keeps the desktop reader pane scroll-contained", () => {
+    const baseCss = loadAllAppCssBaseOnly();
+
+    expect(baseCss).toMatch(/\.research-view__sidebar,\s*\.research-view__reader\s*\{[^}]*min-height:\s*0;[^}]*\}/);
+    expect(baseCss).toMatch(/\.research-view__reader\s*\{[^}]*overflow:\s*auto;[^}]*\}/);
+    expect(baseCss).not.toMatch(/\.research-view__reader\s*\{[^}]*position:\s*(absolute|fixed);[^}]*\}/);
+    expect(baseCss).toMatch(/\.research-view__reader-content\s*\{[^}]*display:\s*flex;[^}]*flex:\s*1(?:\s+1\s+0%)?;[^}]*min-height:\s*0;[^}]*\}/);
+  });
+
+  it("FN-3912: research view content is scrollable on mobile", () => {
+    const css = loadAllAppCss();
+
+    expect(css).toMatch(/@media\s*\(max-width:\s*768px\)\s*\{[\s\S]*?\.research-view\s*\{[^}]*overflow-y:\s*auto;[^}]*padding-bottom:\s*calc\(var\(--space-md\)\s*\+\s*var\(--mobile-nav-height\)\s*\+\s*env\(safe-area-inset-bottom,\s*0px\)\s*\+\s*var\(--standalone-bottom-gap\)\);[^}]*\}/);
+    expect(css).toMatch(/@media\s*\(max-width:\s*768px\)\s*\{[\s\S]*?\.research-view__layout\s*\{[^}]*display:\s*flex;[^}]*flex-direction:\s*column;[^}]*gap:\s*var\(--space-md\);[^}]*\}/);
   });
 });

packages/dashboard/app/components/__tests__/SettingsModal.test.tsx

@@ -183,6 +183,7 @@ const defaultSettings = {
   verificationFixRetries: 2,
   workflowRevisionForkOnScopeMismatch: true,
   recycleWorktrees: false,
+  executorAllowSiblingBranchRename: false,
   worktreeNaming: "random",
   includeTaskIdInCommit: true,
   worktreeInitCommand: "",
@@ -260,6 +261,27 @@ describe("SettingsModal", () => {
     expect(screen.queryByLabelText("Direct merge commit routing")).not.toBeInTheDocument();
   });
 
+  it("persists the legacy sibling branch rename escape hatch in worktree settings", async () => {
+    renderModal();
+    await waitForSettingsModalReady();
+
+    await userEvent.click(screen.getByRole("button", { name: /^Worktrees$/ }));
+
+    const checkbox = screen.getByRole("checkbox", { name: "Allow silent sibling branch rename during executor conflicts" });
+    expect(checkbox).not.toBeChecked();
+
+    await userEvent.click(checkbox);
+    await userEvent.click(screen.getByRole("button", { name: "Save" }));
+
+    await waitFor(() => {
+      expect(mockUpdateSettings).toHaveBeenCalledWith(
+        expect.objectContaining({ executorAllowSiblingBranchRename: true }),
+        undefined,
+      );
+    });
+    expect(screen.getByText(/restores the legacy behavior/i)).toBeInTheDocument();
+  });
+
   beforeEach(() => {
     vi.clearAllMocks();
     clearPluginUiSlotsCache();