Bump actions/checkout from 5 to 6

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Author: dependabot[bot]

.github/workflows/ci_cmake.yml

@@ -49,7 +49,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Configure tests
         run: |

.github/workflows/ci_coverage.yml

@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 

.github/workflows/ci_documentation.yml

@@ -34,12 +34,12 @@ jobs:
     steps:
       - name: Checkout
         if: github.event_name != 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       # pull_request_target does not checkout the merge commit by default
       - name: Checkout
         if: github.event_name == 'pull_request_target'
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           ref: "refs/pull/${{ github.event.number }}/merge"
 

.github/workflows/ci_license.yml

@@ -32,7 +32,7 @@ jobs:
     if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint'
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: REUSE Compliance Check
         uses: fsfe/reuse-action@v6

.github/workflows/ci_linux.yml

@@ -38,7 +38,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main

.github/workflows/ci_macos.yml

@@ -36,7 +36,7 @@ jobs:
         compiler: ["clang-latest", "clang-second-latest", "clang-third-latest", "gcc-latest", "gcc-second-latest", "gcc-third-latest"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup toolchain
         uses: seqan/actions/setup-toolchain@main

.github/workflows/ci_misc.yml

@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Setup cache
         uses: seqan/actions/setup-actions-cache@main

.github/workflows/ci_update_cookbook.yml

@@ -28,7 +28,7 @@ jobs:
     timeout-minutes: 15
     steps:
       - name: Checkout SeqAn3
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           token: ${{ secrets.SEQAN_ACTIONS_PAT }}
 

.github/workflows/cron_api.yml

@@ -37,7 +37,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Configure tests
         run: |

.github/workflows/cron_avx2.yml

@@ -39,7 +39,7 @@ jobs:
       image: ghcr.io/seqan/${{ matrix.compiler }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Configure tests
         run: |