diff --git a/.github/workflows/gemini-cli-bot-brain.yml b/.github/workflows/gemini-cli-bot-brain.yml
index c4743e4479..9632be323a 100644
--- a/.github/workflows/gemini-cli-bot-brain.yml
+++ b/.github/workflows/gemini-cli-bot-brain.yml
@@ -58,6 +58,8 @@ jobs:
       contents: 'read'
       issues: 'read'
       actions: 'read'
+    outputs:
+      sha: ${{ steps.get_sha.outputs.sha }}
     env:
       GEMINI_CLI_TRUST_WORKSPACE: 'true'
     steps:
@@ -84,6 +86,10 @@ jobs:
           fetch-depth: 0
           persist-credentials: false
 
+      - name: 'Get Current SHA'
+        id: 'get_sha'
+        run: echo "sha=$(git rev-parse HEAD)" >> "$GITHUB_OUTPUT"
+
       - name: 'Setup Node.js'
         uses: 'actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020' # ratchet:actions/setup-node@v4
         with:
@@ -296,26 +302,10 @@ jobs:
           permission-pull-requests: 'write'
           permission-issues: 'write'
 
-      - name: 'Determine Checkout Ref'
-        id: 'determine_ref'
-        env:
-          GH_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-          GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'
-          ISSUE_NUMBER: '${{ github.event.issue.number || github.event.inputs.issue_number }}'
-        run: |
-          REF="main"
-          if [ -n "$ISSUE_NUMBER" ]; then
-            PR_HEAD=$(gh pr view "$ISSUE_NUMBER" --repo "${{ github.repository }}" --json headRefName --jq .headRefName 2>/dev/null || echo "")
-            if [ -n "$PR_HEAD" ]; then
-              REF="$PR_HEAD"
-            fi
-          fi
-          echo "ref=$REF" >> "$GITHUB_OUTPUT"
-
       - name: 'Checkout'
         uses: 'actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8' # ratchet:actions/checkout@v5
         with:
-          ref: '${{ steps.determine_ref.outputs.ref }}'
+          ref: '${{ needs.reasoning.outputs.sha }}'
           fetch-depth: 0
           persist-credentials: false
 
@@ -347,7 +337,7 @@ jobs:
             fi
 
             git checkout -B "$BRANCH_NAME"
-            git apply "${{ runner.temp }}/brain-data/bot-changes.patch"
+            git apply --3way --ignore-whitespace "${{ runner.temp }}/brain-data/bot-changes.patch"
             git add .
 
             PR_TITLE="🤖 Gemini Bot Maintenance Update"