ENH: Fix caching-related warnings in GHA build-test-publish CI

Fix caching-related warnings in GHA `build-test-publish` CI:
- Save the `apt-get` cache in a directory other than `/var/lib/apt` to
  avoid permission issues.
- Check if the AFNI cache exists before trying to install it in GitHub
  Actions `build-test-publish` CI workflow.

Fixes:
```
Failed to save: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
```

The full log showing
```
2024-12-19T13:35:45.2830631Z
 [command]/usr/bin/tar --posix -cf cache.tzst --exclude cache.tzst -P -C /home/runner/work/sdcflows/sdcflows --files-from manifest.txt --use-compress-program zstdmt
2024-12-19T13:35:46.5536670Z
 Failed to save: Unable to reserve cache with key afni-v1, another job may be creating this cache. More details: Cache already exists. Scope: refs/heads/master, Key: afni-v1, Version: d04022ae09f8f21b8c0f9f00e4a784b6e510fe6a47d30aa3b0853a42885b92cb
2024-12-19T13:35:46.5924639Z
 Post job cleanup.
2024-12-19T13:35:46.7348688Z
 [command]/usr/bin/tar --posix -cf cache.tzst --exclude cache.tzst -P -C /home/runner/work/sdcflows/sdcflows --files-from manifest.txt --use-compress-program zstdmt
2024-12-19T13:35:46.8326360Z
 /usr/bin/tar: ../../../../../var/lib/apt/lists/lock: Cannot open: Permission denied
2024-12-19T13:35:47.1807249Z
 /usr/bin/tar: ../../../../../var/lib/apt/lists/partial: Cannot open: Permission denied
2024-12-19T13:35:47.2842971Z
 /usr/bin/tar: Exiting with failure status due to previous errors
2024-12-19T13:35:47.2851756Z
 ##[warning]Failed to save: "/usr/bin/tar" failed with error: The process '/usr/bin/tar' failed with exit code 2
```

raised for exmaple in:
https://github.com/nipreps/sdcflows/actions/runs/12413644206

.github/workflows/build-test-publish.yml

@@ -88,7 +88,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/cache@v4
       with:
-        path: /var/lib/apt
+        path: ${{ runner.temp }}/cache-linux
         key: apt-cache-v3
         restore-keys: |
           apt-cache-v3
@@ -102,13 +102,16 @@ jobs:
                         libglu1-mesa-dev libglw1-mesa     \
                         libxm4 build-essential
 
-    - uses: actions/cache@v4
+    - name: Restore cache for AFNI
+      id: cache-afni
+      uses: actions/cache@v4
       with:
         path: /opt/afni
-        key: afni-v1
+        key: afni-v1-${{ python-version }}-${{ matrix.dependencies }}-${{ matrix.marks }}
         restore-keys: |
-          afni-v1
+          afni-v1-
     - name: Install AFNI
+      if: steps.cache-afni.outputs.cache-hit != 'true'
       run: |
         if [[ ! -d "${AFNI_HOME}" ]]; then
           curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries && \