diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 87417153a5..b4b787a283 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -23,7 +23,7 @@ jobs:
         os: [ ubuntu-latest, windows-latest, macos-latest ]
     if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 2
     - uses: actions/cache@v2
diff --git a/.github/workflows/git-repo-sync.yml b/.github/workflows/git-repo-sync.yml
index 2219f2330a..250dd00933 100644
--- a/.github/workflows/git-repo-sync.yml
+++ b/.github/workflows/git-repo-sync.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     continue-on-error: false
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 100
     - name: Setup Environment
diff --git a/.github/workflows/troubleshooting.yml b/.github/workflows/troubleshooting.yml
index d58e0f2aa1..4554ddedf7 100644
--- a/.github/workflows/troubleshooting.yml
+++ b/.github/workflows/troubleshooting.yml
@@ -12,7 +12,7 @@ jobs:
         os: [ ubuntu-latest ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: actions/cache@v2
         with:
           path: |
diff --git a/docs/pages/pmd/userdocs/tools/java-api.md b/docs/pages/pmd/userdocs/tools/java-api.md
index 0deb99a596..36ebb017ea 100644
--- a/docs/pages/pmd/userdocs/tools/java-api.md
+++ b/docs/pages/pmd/userdocs/tools/java-api.md
@@ -66,7 +66,7 @@ public class PmdExample {
     public static void main(String[] args) {
         PMDConfiguration configuration = new PMDConfiguration();
         configuration.setInputPaths("/home/workspace/src/main/java/code");
-        configuration.setRuleSets("rulesets/java/quickstart.xml");
+        configuration.addRuleSet("rulesets/java/quickstart.xml");
         configuration.setReportFormat("xml");
         configuration.setReportFile("/home/workspace/pmd-report.xml");
 
@@ -85,7 +85,7 @@ You can also provide your own custom renderers.
     ```java
     PMDConfiguration configuration = new PMDConfiguration();
     configuration.setMinimumPriority(RulePriority.MEDIUM);
-    configuration.setRuleSets("rulesets/java/quickstart.xml");
+    configuration.addRuleSet("rulesets/java/quickstart.xml");
     ```
     
 2.  Then we configure, which paths to analyze:
@@ -166,7 +166,6 @@ import java.nio.file.Paths;
 import net.sourceforge.pmd.PMDConfiguration;
 import net.sourceforge.pmd.PmdAnalysis;
 import net.sourceforge.pmd.RulePriority;
-import net.sourceforge.pmd.RuleSetLoader;
 import net.sourceforge.pmd.lang.LanguageRegistry;
 import net.sourceforge.pmd.renderers.Renderer;
 import net.sourceforge.pmd.renderers.XMLRenderer;
@@ -176,7 +175,7 @@ public class PmdExample2 {
     public static void main(String[] args) throws IOException {
         PMDConfiguration configuration = new PMDConfiguration();
         configuration.setMinimumPriority(RulePriority.MEDIUM);
-        configuration.setRuleSets("rulesets/java/quickstart.xml");
+        configuration.addRuleSet("rulesets/java/quickstart.xml");
 
         configuration.setInputPaths("/home/workspace/src/main/java/code");
 
@@ -191,7 +190,7 @@ public class PmdExample2 {
 
         try (PmdAnalysis pmd = PmdAnalysis.create(configuration)) {
             // optional: add more rulesets
-            pmd.addRuleSet(RuleSetLoader.fromPmdConfig(configuration).loadFromResource("custom-ruleset.xml"));
+            pmd.addRuleSet(pmd.newRuleSetLoader().loadFromResource("custom-ruleset.xml"));
             // optional: add more files
             pmd.files().addFile(Paths.get("src", "main", "more-java", "ExtraSource.java"));
             // optional: add more renderers
diff --git a/docs/pages/release_notes.md b/docs/pages/release_notes.md
index 59543c4dce..31b9997389 100644
--- a/docs/pages/release_notes.md
+++ b/docs/pages/release_notes.md
@@ -58,6 +58,8 @@ The CLI itself remains compatible, if you run PMD via command-line, no action is
 
 *   apex-performance
     *   [#3773](https://github.com/pmd/pmd/pull/3773): \[apex] EagerlyLoadedDescribeSObjectResult false positives with SObjectField.getDescribe()
+*   core
+    *   [#3299](https://github.com/pmd/pmd/issues/3299): \[core] Deprecate system properties of PMDCommandLineInterface
 
 ### API Changes
 
@@ -76,6 +78,9 @@ The CLI itself remains compatible, if you run PMD via command-line, no action is
   {% jdoc core::PMDConfiguration#addRuleSet(java.lang.String) %},
   and {% jdoc core::PMDConfiguration#getRuleSetPaths() %}.
 * Several members of {% jdoc test::cli.BaseCLITest %} have been deprecated with replacements.
+* Several members of {% jdoc core::cli.PMDCommandLineInterface %} have been explicitly deprecated.
+  The whole class however was deprecated long ago already with 6.30.0. It is internal API and should
+  not be used.
 
 #### Experimental APIs
 
diff --git a/pmd-core/src/main/java/net/sourceforge/pmd/PmdAnalysis.java b/pmd-core/src/main/java/net/sourceforge/pmd/PmdAnalysis.java
index 7f9cf8a0d9..1b74fa5ab8 100644
--- a/pmd-core/src/main/java/net/sourceforge/pmd/PmdAnalysis.java
+++ b/pmd-core/src/main/java/net/sourceforge/pmd/PmdAnalysis.java
@@ -50,7 +50,7 @@ import net.sourceforge.pmd.util.log.internal.SimpleMessageReporter;
  *   config.setInputPaths("src/main/java");
  *   config.prependClasspath("target/classes");
  *   config.setMinimumPriority(RulePriority.HIGH);
- *   config.setRuleSets("rulesets/java/quickstart.xml");
+ *   config.addRuleSet("rulesets/java/quickstart.xml");
  *   config.setReportFormat("xml");
  *   config.setReportFile("target/pmd-report.xml");
  *
@@ -127,8 +127,7 @@ public final class PmdAnalysis implements AutoCloseable {
         FileCollectionUtil.collectFiles(config, pmd.files());
 
         if (config.getReportFormat() != null) {
-            Renderer renderer = config.createRenderer();
-            renderer.setReportFile(config.getReportFile());
+            Renderer renderer = config.createRenderer(true);
             pmd.addRenderer(renderer);
         }