[core] CLI - make sure positional inputPaths are not lost

pmd-cli/src/main/java/net/sourceforge/pmd/cli/commands/internal/AbstractAnalysisPmdSubcommand.java

@@ -7,7 +7,6 @@ package net.sourceforge.pmd.cli.commands.internal;
 import java.net.URI;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.ArrayList;
 import java.util.List;
 
 import net.sourceforge.pmd.AbstractConfiguration;
@@ -34,6 +33,14 @@ public abstract class AbstractAnalysisPmdSubcommand<C extends AbstractConfigurat
             arity = "1..*", split = ",")
     protected List<Path> inputPaths;
 
+    @Parameters(arity = "*", description = "Path to a source file, or directory containing source files to analyze. "
+            + "Equivalent to using --dir.")
+    // Note: we can't directly use inputPaths here, because "--dir" might be specified later in the
+    // command line. And PicoCli will then initialize the field inputPaths with a fresh empty List, replacing
+    // anything what was added before.So we need to combine the two lists in #validate()
+    private List<Path> positionalInputPaths;
+
+
     @Option(names = "--file-list",
             description =
                 "Path to a file containing a list of files to analyze, one path per line. "
@@ -50,16 +57,6 @@ public abstract class AbstractAnalysisPmdSubcommand<C extends AbstractConfigurat
                     + "Disable this option with '--no-fail-on-violation' to exit with 0 instead and just write the report.",
             defaultValue = "true", negatable = true)
     protected boolean failOnViolation;
-    
-    @Parameters(arity = "*", description = "Path to a source file, or directory containing source files to analyze. "
-            + "Equivalent to using --dir.")
-    public void setInputPaths(final List<Path> inputPaths) {
-        if (this.inputPaths == null) {
-            this.inputPaths = new ArrayList<>();
-        }
-        
-        this.inputPaths.addAll(inputPaths);
-    }
 
     protected List<Path> relativizeRootPaths;
 
@@ -84,6 +81,14 @@ public abstract class AbstractAnalysisPmdSubcommand<C extends AbstractConfigurat
     protected final void validate() throws ParameterException {
         super.validate();
 
+        if (positionalInputPaths != null) {
+            if (inputPaths == null) {
+                inputPaths = positionalInputPaths;
+            } else {
+                inputPaths.addAll(positionalInputPaths);
+            }
+        }
+
         if ((inputPaths == null || inputPaths.isEmpty()) && uri == null && fileListPath == null) {
             throw new ParameterException(spec.commandLine(),
                                          "Please provide a parameter for source root directory (--dir or -d), "

pmd-cli/src/test/java/net/sourceforge/pmd/cli/CpdCliTest.java

@@ -119,12 +119,19 @@ class CpdCliTest extends BaseCliTest {
     }
 
     @Test
-    void testWrongCliOptionResultsInErrorLogging() throws Exception {
+    void testWrongCliOptionResultsInErrorLoggingAfterDir() throws Exception {
         // --ignore-identifiers doesn't take an argument anymore - it is interpreted as a file for inputPaths
         final CliExecutionResult result = runCli(VIOLATIONS_FOUND, "--minimum-tokens", "34", "--dir", SRC_DIR, "--ignore-identifiers", "false");
         result.checkStdErr(containsString("No such file false"));
     }
 
+    @Test
+    void testWrongCliOptionResultsInErrorLoggingBeforeDir() throws Exception {
+        // --ignore-identifiers doesn't take an argument anymore - it is interpreted as a file for inputPaths
+        final CliExecutionResult result = runCli(VIOLATIONS_FOUND, "--minimum-tokens", "34", "--ignore-identifiers", "false", "--dir", SRC_DIR);
+        result.checkStdErr(containsString("No such file false"));
+    }
+
     @Test
     void testFindJavaDuplication() throws Exception {
         runCli(VIOLATIONS_FOUND, "--minimum-tokens", "7", "--dir", SRC_DIR)

pmd-cli/src/test/java/net/sourceforge/pmd/cli/commands/internal/BaseCommandTest.java

@@ -15,7 +15,7 @@ import org.hamcrest.Matchers;
 import picocli.CommandLine;
 import picocli.CommandLine.ParseResult;
 
-abstract class BaseCommandTest<T> {
+abstract class BaseCommandTest<T extends AbstractAnalysisPmdSubcommand<?>> {
 
     protected abstract T createCommand();
     
@@ -30,6 +30,7 @@ abstract class BaseCommandTest<T> {
     protected T setupAndParse(final String... params) {
         final T cmd = createCommand();
         final ParseResult parseResult = parseCommand(cmd, params);
+        cmd.validate();
 
         assertThat(parseResult.errors(), Matchers.empty());