docs: make minor comment improvements [ci skip]

Author: marco-brandizi

.github/workflows/deploy.yml

@@ -1,5 +1,7 @@
 # The GitHub Actions file
 
+# This is based on the knetminer-ci template, see there for details.
+
 name: Standard Build
 
 on:
@@ -55,15 +57,11 @@ jobs:
         key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
         restore-keys: ${{ runner.os }}-m2
 
-    # Avoids re-listing all the secrets again. As they recommend, use the commit hash to point to 
-    # an exact version, using tags might be compromised by malicious commits.
-    #
-    # See knetminer-ci docs for a list of secrets and other variables we use.
-    #
-    - name: Forward all GH secrets to env
-      uses: oNaiPs/secrets-to-env-action@75f319b3c8c926ac2eabcca34daa6cf531daf32f
-      with:
-        secrets: ${{ toJSON(secrets) }}
+    - name: Forward secrets to env vars
+      env:
+        _SECRETS_JS_STR: ${{ toJSON(secrets) }}
+      run: |
+        echo "$_SECRETS_JS_STR" | jq -r 'to_entries[] | "\(.key)<<EOF\n\(.value)\nEOF"' >> $GITHUB_ENV    
 
     - name: Build
       # You still need this for variables that aren't secrets, but better than nothing

ci-build-v2/java-maven/build.sh

@@ -21,7 +21,7 @@ function stage_build_local
 
 printf "== Installing ci-build scripts and then running the build\n"
 
-# TODO: DO USE a version tag in place of main, DO MAKE your builds stable and predictable
+# DO USE a version tag in place of main, DO MAKE your builds stable and predictable
 ci_build_url_base="https://raw.githubusercontent.com/KnetMiner/knetminer-ci/refs/tags/1.0"
 script_url="$ci_build_url_base/ci-build-v2/install.sh"
 . <(curl --fail-with-body -o - "$script_url") "$ci_build_url_base" java-maven

pom.xml

@@ -219,7 +219,7 @@
 		  uk.ac.ebi.utils.opt.json
 		-->
 		<dependency>
-			<groupId> tools.jackson.dataformat </groupId>
+			<groupId>tools.jackson.dataformat</groupId>
 			<artifactId>jackson-dataformat-yaml</artifactId>
 			<version>3.1.2</version>
 		</dependency>