fix(flex-edge): shellcheck complaints (#437)

Author: kojiromike

.github/workflows/shellcheck.yml

@@ -8,7 +8,8 @@ on:
     # the paths in sync and the exclusion logic.
     paths:
       # Include all shell scripts except those in docker/openemr/obsolete/
-      - '{!docker/openemr/obsolete/,}**.sh'
+      - '**.sh'
+      - '**.source'
       - '.github/workflows/shellcheck.yml'
       - 'docker/openemr/flex-*/utilities/devtools'
       - 'kubernetes/kub-down'
@@ -19,12 +20,16 @@ on:
       - 'utilities/openemr-env-installer/openemr-env-installer'
       - 'utilities/openemr-env-migrator/openemr-env-migrator'
       - 'utilities/openemr-monitor/monitor-installer'
+      # Exclude everything in obsolete.
+      # This needs to be last.
+      - '!docker/openemr/obsolete/**'
   pull_request:
     branches:
       - master
     paths:
       # Include all shell scripts except those in docker/openemr/obsolete/
-      - '{!docker/openemr/obsolete/,}**.sh'
+      - '**.sh'
+      - '**.source'
       - '.github/workflows/shellcheck.yml'
       - 'docker/openemr/flex-*/utilities/devtools'
       - 'kubernetes/kub-down'
@@ -35,6 +40,9 @@ on:
       - 'utilities/openemr-env-installer/openemr-env-installer'
       - 'utilities/openemr-env-migrator/openemr-env-migrator'
       - 'utilities/openemr-monitor/monitor-installer'
+      # Exclude everything in obsolete.
+      # This needs to be last.
+      - '!docker/openemr/obsolete/**'
 jobs:
   shellcheck:
     name: ShellCheck
@@ -59,8 +67,8 @@ jobs:
           # See https://github.com/tj-actions/changed-files/blob/v46/README.md#inputs-%EF%B8%8F
           # for tj-actions/changed-files specific syntax
           files: |
-            !docker/openemr/obsolete/**
             **.sh
+            **.source
             docker/openemr/flex-*/utilities/devtools
             kubernetes/kub-down
             kubernetes/kub-up
@@ -70,6 +78,7 @@ jobs:
             utilities/openemr-env-installer/openemr-env-installer
             utilities/openemr-env-migrator/openemr-env-migrator
             utilities/openemr-monitor/monitor-installer
+            !docker/openemr/obsolete/**
       - name: Create unique files list
         id: unique-files
         run: |
@@ -92,9 +101,11 @@ jobs:
             # Use the same paths as in the on.push and on.pull_request sections
             # to ensure we only check shell files.
             # Use globstar to find shell files in subdirectories.
-            shopt -s globstar
-            files_to_check=(
+            # We can't easily exclude obsolete here, so we exclude it later...
+            shopt -s globstar nullglob
+            files_to_check+=(
               **/*.sh
+              **/*.source
               docker/openemr/flex-*/utilities/devtools
               kubernetes/kub-down
               kubernetes/kub-up
@@ -126,6 +137,11 @@ jobs:
           echo "files=${unique_files[*]}" >> "$GITHUB_OUTPUT"
       - name: Run shellcheck on unique files
         if: ${{ steps.unique-files.outputs.files != '' }}
+        # Pipefail is somehow only enabled when we explicitly
+        # specify the shell as bash, even though bash is the
+        # default shell. I would complain further, but
+        # this kind of inconsistency is very shell-like anyway.
+        shell: bash
         run: |
           shellcheck --check-sourced --external-sources --format=checkstyle ${{ steps.unique-files.outputs.files }} | tee checkstyle-shellcheck.xml
       - uses: staabm/annotate-pull-request-from-checkstyle-action@v1