docs(agents): add initial guidelines for coding agents

.github/workflows/binaries.yml

@@ -375,12 +375,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number
@@ -421,10 +425,6 @@ jobs:
         include:
           - os: macos-15
             displayName: macOS (ARM64)
-            suffix: '_arm64'
-          - os: macos-15-intel  # intel image
-            displayName: macOS
-            suffix: ''
     runs-on: ${{ matrix.os }}
     steps:
       - name: Download from GitHub workflow artifacts store (macOS)

.github/workflows/gource.yml

@@ -21,9 +21,9 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - title: 'JabRef v6.0 (in development) | more information at contribute.jabref.org'
-            # Last alpha release 2025-04-27, but want to have some seconds before
-            start: '2025-04-15'
+          - title: 'JabRef v6.0 (since alpha.3) | more information at contribute.jabref.org'
+            # Last alpha release 2025-10-30, but want to have some seconds before
+            start: '2025-10-29'
             end: ''
             file: 'jabref-v6.0-dev.mp4'
 #          - title: 'JabRef v6.0-alpha2 | more information at contribute.jabref.org'

.github/workflows/link-issue.yml

@@ -26,12 +26,16 @@ jobs:
       issue_number: ${{ steps.get_issue_number.outputs.ticketNumber }}
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number

.github/workflows/on-pr-changes-requested-check.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
-      actions: read
+      actions: write
     steps:
       - name: Create pr_number.txt
         run: echo "${{ github.event.pull_request.number }}" > pr_number.txt

.github/workflows/on-pr-changes-requested-move-labels.yml

@@ -15,10 +15,11 @@ jobs:
       contents: read
     steps:
       - name: Download artifact from triggering run
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           run-id: ${{ github.event.workflow_run.id }}
           name: pr_number
+          github-token: ${{ secrets.GITHUB_TOKEN }}
         continue-on-error: true
       - name: Check for pr_number.txt
         id: check

.github/workflows/on-pr-closed.yml

@@ -25,12 +25,16 @@ jobs:
       issue_number: ${{ steps.get_issue_number.outputs.ticketNumber }}
     steps:
       - name: echo PR data
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          PR_BODY: ${{ github.event.pull_request.body }}
         run: |
-          echo "PR Number: ${{ github.event.pull_request.number }}"
-          echo "PR URL: ${{ github.event.pull_request.html_url }}"
+          echo "PR Number: $PR_NUMBER"
+          echo "PR URL: $PR_URL"
           cat <<EOF
           PR Body:
-          ${{ github.event.pull_request.body }}
+          $PR_BODY
           EOF
       - name: Determine issue number
         id: get_issue_number

.github/workflows/on-pr-opened-updated-move-labels.yml

@@ -15,7 +15,7 @@ jobs:
       contents: read
     steps:
       - name: Download artifact from triggering run
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v6
         with:
           run-id: ${{ github.event.workflow_run.id }}
           name: pr_number

.jbang/JabKitLauncher.java

@@ -36,6 +36,7 @@
 // DEPS com.github.jabref:jabref:main-SNAPSHOT
 //DEPS io.github.darvil82:terminal-text-formatter:2.2.0
 //DEPS info.picocli:picocli:4.7.7
+//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 
 import org.jabref.JabKit;
 

.jbang/JabLsLauncher.java

@@ -50,6 +50,7 @@
 //DEPS org.slf4j:slf4j-api:2.0.17
 //DEPS org.tinylog:slf4j-tinylog:2.7.0
 //DEPS org.tinylog:tinylog-impl:2.7.0
+//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabLsLauncher {

.jbang/JabSrvLauncher.java

@@ -73,12 +73,12 @@
 //DEPS org.bouncycastle:bcprov-jdk18on:1.82
 //DEPS com.konghq:unirest-modules-gson:4.5.1
 //DEPS jakarta.ws.rs:jakarta.ws.rs-api:4.0.0
-//DEPS org.glassfish.jersey.core:jersey-server:3.1.11
-//DEPS org.glassfish.jersey.inject:jersey-hk2:3.1.11
+//DEPS org.glassfish.jersey.core:jersey-server:4.0.0
+//DEPS org.glassfish.jersey.inject:jersey-hk2:4.0.0
 //DEPS org.glassfish.hk2:hk2-api:3.1.1
 //DEPS org.glassfish.hk2:hk2-utils:3.1.1
 //DEPS org.glassfish.hk2:hk2-locator:3.1.1
-//DEPS org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.11
+//DEPS org.glassfish.jersey.containers:jersey-container-grizzly2-http:4.0.0
 //DEPS org.glassfish.grizzly:grizzly-http-server:4.0.2
 //DEPS org.glassfish.grizzly:grizzly-framework:4.0.2
 //DEPS jakarta.validation:jakarta.validation-api:3.1.1
@@ -88,6 +88,7 @@
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.5.0
 //DEPS de.undercouch:citeproc-java:3.4.0
+//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabSrvLauncher {

.markdownlint.yml

@@ -6,3 +6,6 @@ MD013: false
 MD033:
   # we have <a> tags with ids and superscript
   allowed_elements: ['a', 'kbd', 'sup']
+
+exclude:
+    - AGENTS.md