fix(naming): preserve branch prompt overrides

src/main/persistence.test.ts

@@ -2483,7 +2483,7 @@ describe('Store', () => {
     })
     expect(persisted.settings.sourceControlAi.actions.branchName).toEqual({
       agentId: 'claude',
-      commandInputTemplate: '{basePrompt}\n\nRollback commit prompt'
+      commandInputTemplate: 'Rollback commit prompt\n\n{basePrompt}'
     })
   })
 

src/main/text-generation/commit-message-text-generation.test.ts

@@ -1853,7 +1853,7 @@ describe('generateBranchNameFromContext', () => {
     })
   })
 
-  it('includes the branch-name custom prompt in the generated prompt', async () => {
+  it('keeps branch-name guidance first without dropping the output contract', async () => {
     let prompt = ''
     await generateBranchNameFromContext(
       { firstPrompt: 'Fix login flow' },
@@ -1861,7 +1861,8 @@ describe('generateBranchNameFromContext', () => {
         agentId: 'custom',
         model: '',
         customAgentCommand: 'agent',
-        customPrompt: 'Prefer auth terminology.'
+        customPrompt: 'Prefer auth terminology.',
+        commandInputTemplate: 'Prefer auth terminology.\n\n{basePrompt}'
       },
       {
         kind: 'remote',
@@ -1882,6 +1883,8 @@ describe('generateBranchNameFromContext', () => {
     expect(prompt.startsWith('Prefer auth terminology.')).toBe(true)
     expect(prompt).toContain('Prefer auth terminology.')
     expect(prompt).not.toContain('Additional user prompt:')
+    expect(prompt).toContain('Generate a short git branch name')
+    expect(prompt).toContain('Output ONLY the branch name on a single line')
   })
 })
 

src/shared/branch-name-from-work.test.ts

@@ -127,6 +127,8 @@ describe('buildBranchNamePrompt', () => {
     expect(prompt.startsWith('Prefer product nouns.')).toBe(true)
     expect(prompt).not.toContain('Additional user prompt:')
     expect(prompt).not.toContain('Rules:')
+    expect(prompt).toContain('Generate a git branch name')
+    expect(prompt).toContain('Output ONLY the branch name on a single line')
     expect(prompt).toContain('Add a logout button')
   })
 })

src/shared/branch-name-from-work.ts

@@ -113,13 +113,14 @@ export function buildBranchNamePrompt(context: BranchNameWorkContext, customProm
   // override owns style rather than sitting under a prescriptive default.
   if (prompt) {
     sections.push(prompt, '')
-  } else {
-    sections.push(
-      'Generate a short git branch name that summarizes the coding task described below.',
-      'Output ONLY the branch name on a single line, nothing else.',
-      ''
-    )
   }
+  sections.push(
+    prompt
+      ? 'Generate a git branch name that summarizes the coding task described below.'
+      : 'Generate a short git branch name that summarizes the coding task described below.',
+    'Output ONLY the branch name on a single line, nothing else.',
+    ''
+  )
   sections.push('User request:', context.firstPrompt.trim())
   const assistant = context.assistantMessage?.trim()
   if (assistant) {

src/shared/source-control-ai.test.ts

@@ -313,11 +313,19 @@ describe('source-control AI resolution', () => {
       }).params.customPrompt
     ).toBe('Repo commit style')
     expect(resolve('branchName').params.customPrompt).toBe('Global branch style')
+    expect(resolve('branchName').params.commandInputTemplate).toBe(
+      'Global branch style\n\n{basePrompt}'
+    )
     expect(
       resolve('branchName', {
         instructionsByOperation: { branchName: 'Repo branch style' }
       }).params.customPrompt
     ).toBe('Repo branch style')
+    expect(
+      resolve('branchName', {
+        instructionsByOperation: { branchName: 'Repo branch style' }
+      }).params.commandInputTemplate
+    ).toBe('Repo branch style\n\n{basePrompt}')
   })
 
   it('does not treat null repo instructions as configured overrides', () => {
@@ -368,6 +376,12 @@ describe('source-control AI resolution', () => {
     expect(migrated.instructionsByOperation.commitMessage).toBe('Legacy commit prompt')
     expect(migrated.instructionsByOperation.pullRequest).toBe('')
     expect(migrated.instructionsByOperation.branchName).toBe('Legacy commit prompt')
+    expect(migrated.actions?.commitMessage?.commandInputTemplate).toBe(
+      '{basePrompt}\n\nLegacy commit prompt'
+    )
+    expect(migrated.actions?.branchName?.commandInputTemplate).toBe(
+      'Legacy commit prompt\n\n{basePrompt}'
+    )
   })
 
   it('merges legacy commit-message updates without wiping PR-only settings', () => {
@@ -702,7 +716,7 @@ describe('source-control AI resolution', () => {
           commandInputTemplate: '{basePrompt}'
         },
         branchName: {
-          commandInputTemplate: '{basePrompt}\n\nbranch style'
+          commandInputTemplate: 'branch style\n\n{basePrompt}'
         }
       },
       prCreationDefaults: {

src/shared/source-control-ai.ts

@@ -296,13 +296,15 @@ export function normalizeRepoSourceControlAiOverrides(
   const migratedActionOverrides = { ...actionOverrides }
   for (const operation of SOURCE_CONTROL_TEXT_ACTION_IDS) {
     const instruction = instructionsByOperation?.[operation]
+    const existingTemplate = migratedActionOverrides[operation]?.commandInputTemplate
     if (
       typeof instruction === 'string' &&
-      migratedActionOverrides[operation]?.commandInputTemplate === undefined
+      (existingTemplate === undefined ||
+        isLegacyBranchInstructionTemplate(operation, instruction, existingTemplate))
     ) {
       migratedActionOverrides[operation] = {
         ...migratedActionOverrides[operation],
-        commandInputTemplate: commandTemplateFromInstruction(instruction)
+        commandInputTemplate: commandTemplateFromOperationInstruction(operation, instruction)
       }
     }
   }
@@ -324,6 +326,35 @@ function commandTemplateFromInstruction(instruction: string | null | undefined):
   return ['{basePrompt}', '', trimmed].join('\n')
 }
 
+function commandTemplateFromOperationInstruction(
+  operation: SourceControlAiOperation,
+  instruction: string | null | undefined
+): string {
+  const trimmed = instruction?.trim()
+  if (!trimmed) {
+    return '{basePrompt}'
+  }
+  // Why: branch naming instructions define naming style, so they must precede
+  // the general built-in prompt. Other operations retain their released order.
+  return operation === 'branchName'
+    ? [trimmed, '', '{basePrompt}'].join('\n')
+    : commandTemplateFromInstruction(trimmed)
+}
+
+function isLegacyBranchInstructionTemplate(
+  operation: SourceControlAiOperation,
+  instruction: string | null | undefined,
+  template: string | null | undefined
+): boolean {
+  // Why: reorder only the exact template older settings derived automatically;
+  // a user-authored command template remains authoritative.
+  return (
+    operation === 'branchName' &&
+    Boolean(instruction?.trim()) &&
+    template === commandTemplateFromInstruction(instruction)
+  )
+}
+
 function actionRecipeFromLegacyCommitMessageAi(legacy: CommitMessageAiSettings): {
   agentId?: TuiAgent | CustomAgentId | null
   commandInputTemplate: string
@@ -400,7 +431,10 @@ function shouldImportLegacyBranchPrompt(
   projectedLegacy: CommitMessageAiSettings
 ): boolean {
   const branchRecipe = readSourceControlActionDefault(base.actions, 'branchName')
-  const projectedTemplate = commandTemplateFromInstruction(projectedLegacy.customPrompt)
+  const projectedTemplate = commandTemplateFromOperationInstruction(
+    'branchName',
+    projectedLegacy.customPrompt
+  )
   return (
     branchRecipe.commandInputTemplate === undefined ||
     branchRecipe.commandInputTemplate ===
@@ -473,7 +507,13 @@ export function sourceControlAiSettingsFromLegacy(
     actions: {
       ...defaults.actions,
       commitMessage: legacyActionRecipe,
-      branchName: legacyActionRecipe
+      branchName: {
+        ...legacyActionRecipe,
+        commandInputTemplate: commandTemplateFromOperationInstruction(
+          'branchName',
+          legacy.customPrompt
+        )
+      }
     }
   }
 }
@@ -640,7 +680,12 @@ export function mergeLegacyCommitMessageAiIntoSourceControlAi(
                     ? applyLegacyAgentToActionRecipe(base.actions?.branchName, legacy.agentId)
                     : base.actions?.branchName),
                   ...(shouldMergeBranchPrompt
-                    ? { commandInputTemplate: legacyActionRecipe.commandInputTemplate }
+                    ? {
+                        commandInputTemplate: commandTemplateFromOperationInstruction(
+                          'branchName',
+                          legacy.customPrompt
+                        )
+                      }
                     : {})
                 }
               }
@@ -693,15 +738,21 @@ export function normalizeSourceControlAiSettings(
       const existing = readSourceControlActionDefault(normalizedActions, actionId)
       const instruction = base.instructionsByOperation?.[actionId]
       const legacyInstruction = actionId === 'commitMessage' ? legacy?.customPrompt : undefined
+      const resolvedInstruction = instruction ?? legacyInstruction
       const instructionTemplate =
         instruction || legacyInstruction
-          ? commandTemplateFromInstruction(instruction ?? legacyInstruction)
+          ? commandTemplateFromOperationInstruction(actionId, resolvedInstruction)
           : undefined
       const shouldApplyInstructionTemplate =
         instructionTemplate !== undefined &&
         (existing.commandInputTemplate === undefined ||
           existing.commandInputTemplate ===
-            DEFAULT_SOURCE_CONTROL_ACTION_COMMAND_TEMPLATES[actionId])
+            DEFAULT_SOURCE_CONTROL_ACTION_COMMAND_TEMPLATES[actionId] ||
+          isLegacyBranchInstructionTemplate(
+            actionId,
+            resolvedInstruction,
+            existing.commandInputTemplate
+          ))
       return [
         actionId,
         {
@@ -1048,7 +1099,7 @@ function resolveActionRecipeForTextOperation(
   )
   const fallbackTemplate =
     repoInstruction !== undefined
-      ? commandTemplateFromInstruction(repoInstruction)
+      ? commandTemplateFromOperationInstruction(operation, repoInstruction)
       : resolveSourceControlActionCommandTemplate(source.actions, operation)
   const repoTemplate =
     typeof repoRecipe?.commandInputTemplate === 'string'