diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 183196bb..942b43a9 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -27,12 +27,12 @@ jobs:
     steps:
     - name: Add reaction
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
         comment-id: ${{ github.event.client_payload.github.payload.comment.id }}
-        reaction-type: hooray
+        reactions: hooray
     - name: Set galaxy fork and branch
       id: get-fork-branch
       run: |
@@ -43,7 +43,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ steps.get-fork-branch.outputs.fork }}/galaxy refs/heads/${{ steps.get-fork-branch.outputs.branch }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -56,9 +56,9 @@ jobs:
     # are not available as wheels, pip will build a wheel for them, which can be cached.
     - name: Install wheel
       run: pip install wheel
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -75,7 +75,7 @@ jobs:
         echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})'
 
   lint:
-    name: Check for missing containers
+    name: Lint tool-list
     needs: setup
     if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }}
     runs-on: ubuntu-latest
@@ -84,10 +84,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -101,10 +101,11 @@ jobs:
       id: lint
       with:
         mode: lint
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-        additional-planemo-options: --biocontainers -s tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata
-    - uses: actions/upload-artifact@v4
+        additional-planemo-options: --biocontainers --skip tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,version_bumped
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -131,12 +132,10 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    # checkout the repository
-    # and use it as the current working directory
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -163,7 +162,7 @@ jobs:
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
         test_timeout: 900
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -182,10 +181,10 @@ jobs:
     # This job runs on Linux
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
       with:
         path: artifacts
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -200,10 +199,12 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v4
+        markdown-report: true
+    - uses: actions/upload-artifact@v5
       with:
         name: 'All tool test results'
         path: upload
+    - run: cat upload/tool_test_output.md >> $GITHUB_STEP_SUMMARY
     - name: Create URL to the run output
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
       id: vars
@@ -211,7 +212,7 @@ jobs:
 
     - name: Create comment
       if: ${{ github.event.client_payload.slash_command.command == 'run-all-tool-tests' }}
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 31e5719c..6e23b8ad 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -59,7 +59,7 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -80,9 +80,10 @@ jobs:
       run: pip install wheel
     - name: Install flake8
       run: pip install flake8 flake8-import-order
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
       uses: galaxyproject/planemo-ci-action@v1
       id: discover
@@ -113,10 +114,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -126,23 +127,24 @@ jobs:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}
 
-    - name: Set fail level for pull request
-      if: ${{ github.event_name == 'pull_request' }}
-      run:
-        echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV"
-    - name: Set fail level for merge
+    - name: Set skip version check for push event (i.e. merge to main)
       if: ${{ github.event_name != 'pull_request' }}
       run:
-        echo "FAIL_LEVEL=error" >> "$GITHUB_ENV"
+        echo "EXTRA_SKIP=--skip version_bumped" >> "$GITHUB_ENV"
+    - name: Set no skip for pull_request events
+      if: ${{ github.event_name == 'pull_request' }}
+      run:
+        echo "EXTRA_SKIP=" >> "$GITHUB_ENV"
     - name: Planemo lint
       uses: galaxyproject/planemo-ci-action@v1
       id: lint
       with:
         mode: lint
-        fail-level: ${{ env.FAIL_LEVEL }}
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
-    - uses: actions/upload-artifact@v4
+        additional-planemo-options: ${{ env.EXTRA_SKIP }}
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Tool linting output'
@@ -159,10 +161,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -175,7 +177,7 @@ jobs:
       run: pip install flake8 flake8-import-order
     - name: Flake8
       run: echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' flake8 --output-file pylint_report.txt --tee
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'Python linting output'
@@ -191,9 +193,9 @@ jobs:
         os: [ubuntu-24.04]
         r-version: ['release']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
+        persist-credentials: false
     - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
@@ -214,7 +216,7 @@ jobs:
         echo '${{ needs.setup.outputs.repository-list }}' | xargs -d '\n' -n 1 ./.github/styler.R --dry off
         git status
         git diff --exit-code | tee rlint_report.txt
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'R linting output'
@@ -226,9 +228,10 @@ jobs:
     if: ${{ github.event_name == 'pull_request' && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
+        persist-credentials: false
     - name: Check file sizes
       run: |
         touch file_size_report.txt
@@ -241,7 +244,7 @@ jobs:
           cat file_size_report.txt
           exit 1
         fi
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       if: ${{ failure() }}
       with:
         name: 'File size report'
@@ -269,10 +272,10 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -304,8 +307,8 @@ jobs:
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         galaxy-slots: ${{ steps.cpu-cores.outputs.count }}
         # Limit each test to 15 minutes
-        test_timeout: 1800
-    - uses: actions/upload-artifact@v4
+        test_timeout: 900
+    - uses: actions/upload-artifact@v5
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -324,10 +327,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/download-artifact@v4
+    - uses: actions/download-artifact@v6
       with:
         path: artifacts
-    - uses: actions/setup-python@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -343,7 +346,7 @@ jobs:
         mode: combine
         html-report: true
         markdown-report: true
-    - uses: actions/upload-artifact@v4
+    - uses: actions/upload-artifact@v5
       with:
         name: 'All tool test results'
         path: upload
@@ -355,7 +358,8 @@ jobs:
         mode: check
     - name: Check if all test chunks succeeded
       run: |
-        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        ls artifacts/
+        NFILES=$(find artifacts/ -name "tool_test_output.json" | wc -l)
         if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
           exit 1
         fi
@@ -370,10 +374,10 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
       with:
-        fetch-depth: 1
-    - uses: actions/setup-python@v5
+        persist-credentials: false
+    - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
@@ -401,22 +405,22 @@ jobs:
   deploy-report:
     name: Report deploy status
     needs: [deploy]
-    if: ${{ always() && needs.deploy.result != 'success' && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
+    if: ${{ always() && (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' ) && github.repository_owner == 'galaxyproject' }}
     runs-on: ubuntu-latest
     steps:
     # report to the PR if deployment failed
     - name: Get PR object
-      uses: 8BitJonny/gh-get-current-pr@2.2.0
+      uses: 8BitJonny/gh-get-current-pr@4.0.0
       id: getpr
       with:
         sha: ${{ github.event.after }}
     - name: Create comment
-      uses: peter-evans/create-or-update-comment@v4
+      uses: peter-evans/create-or-update-comment@v5
       with:
         token: ${{ secrets.PAT }}
         issue-number: ${{ steps.getpr.outputs.number }}
         body: |
-          Attention: deployment ${{ needs.deploy.result }}!
+          Deployment status: **${{ needs.deploy.result }}**
 
           https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}
 
diff --git a/.github/workflows/slash.yaml b/.github/workflows/slash.yaml
index 838257cb..53a41229 100644
--- a/.github/workflows/slash.yaml
+++ b/.github/workflows/slash.yaml
@@ -8,7 +8,7 @@ jobs:
     steps:
       - name: Slash Command Dispatch
         if: github.repository_owner == 'galaxyproject'
-        uses: peter-evans/slash-command-dispatch@v3
+        uses: peter-evans/slash-command-dispatch@v5
         with:
           token: ${{ secrets.PAT }}
           commands: |