From cc9ca97a346ab5e40a3852768dd2971d788b4865 Mon Sep 17 00:00:00 2001
From: Roberto Perez Alcolea <rperezalcolea@netflix.com>
Date: Wed, 22 Jul 2026 19:08:35 -0700
Subject: [PATCH] Fix ClojureCompile including non-Clojure files as source

  Config-cache support (14.0.2) replaced the filtered SourceDirectorySet
  (set.clojure, restricted to **/*.clj, **/*.cljs, **/*.cljc) with a raw
  project.file(src/.../clojure) to avoid serializing the SourceSet
  object graph. SourceDirectoryTask.getSource() then turned that
  directory into an unfiltered FileTree, so any non-Clojure file sitting
  in the source directory (e.g. a README.md) got passed to the Clojure
  compiler and broke the build.

  Restore the extension filter in SourceDirectoryTask.getSource() so
  only Clojure files are treated as compile/test/run/doc source, while
  keeping srcDirs as plain File objects for classpath purposes and
  configuration-cache compatibility.
---
 gradle.lockfile                               | 12 ++++----
 .../utils/tasks/SourceDirectoryTask.groovy    |  4 ++-
 ...nNebulaClojurePluginIntegrationSpec.groovy | 30 +++++++++++++++++++
 3 files changed, 39 insertions(+), 7 deletions(-)

diff --git a/gradle.lockfile b/gradle.lockfile
index ef28304..b941e60 100644
--- a/gradle.lockfile
+++ b/gradle.lockfile
@@ -6,8 +6,8 @@ com.jcraft:jzlib:1.1.2=integTestRuntimeClasspath,testRuntimeClasspath
 com.netflix.nebula:gradle-contacts-plugin:8.0.0=integTestRuntimeClasspath,testRuntimeClasspath
 com.netflix.nebula:gradle-info-plugin:16.0.0=integTestRuntimeClasspath,testRuntimeClasspath
 com.netflix.nebula:nebula-gradle-interop:2.3.0=integTestRuntimeClasspath,testRuntimeClasspath
-com.netflix.nebula:nebula-publishing-plugin:23.0.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
-com.netflix.nebula:nebula-test:11.12.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+com.netflix.nebula:nebula-publishing-plugin:23.1.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+com.netflix.nebula:nebula-test:12.5.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
 com.perforce:p4java:2015.2.1365273=integTestRuntimeClasspath,testRuntimeClasspath
 io.leangen.geantyref:geantyref:1.3.16=integTestRuntimeClasspath,testRuntimeClasspath
 junit:junit:4.13.2=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
@@ -29,10 +29,10 @@ org.hamcrest:hamcrest:3.0=integTestCompileClasspath,integTestRuntimeClasspath,te
 org.jetbrains.kotlin:kotlin-stdlib:2.1.0=integTestRuntimeClasspath,testRuntimeClasspath
 org.jetbrains:annotations:13.0=integTestRuntimeClasspath,testRuntimeClasspath
 org.jspecify:jspecify:1.0.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
-org.junit.platform:junit-platform-commons:1.14.3=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
-org.junit.platform:junit-platform-engine:1.14.3=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
-org.junit.platform:junit-platform-launcher:1.14.3=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
-org.junit:junit-bom:5.14.3=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+org.junit.platform:junit-platform-commons:1.14.4=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+org.junit.platform:junit-platform-engine:1.14.4=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+org.junit.platform:junit-platform-launcher:1.14.4=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
+org.junit:junit-bom:5.14.4=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
 org.objenesis:objenesis:2.4=integTestRuntimeClasspath,testRuntimeClasspath
 org.opentest4j:opentest4j:1.3.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
 org.spockframework:spock-bom:2.4-groovy-4.0=integTestCompileClasspath,integTestRuntimeClasspath,testCompileClasspath,testRuntimeClasspath
diff --git a/src/main/groovy/nebula/plugin/utils/tasks/SourceDirectoryTask.groovy b/src/main/groovy/nebula/plugin/utils/tasks/SourceDirectoryTask.groovy
index 706a647..94a143f 100644
--- a/src/main/groovy/nebula/plugin/utils/tasks/SourceDirectoryTask.groovy
+++ b/src/main/groovy/nebula/plugin/utils/tasks/SourceDirectoryTask.groovy
@@ -156,6 +156,8 @@ class SourceDirectoryTask extends DefaultTask {
     @IgnoreEmptyDirectories
     @PathSensitive(PathSensitivity.RELATIVE)
     def FileTree getSource() {
-        objectFactory.fileCollection().from(srcDirs).asFileTree
+        objectFactory.fileCollection().from(srcDirs).asFileTree.matching {
+            include "**/*.clj", "**/*.cljs", "**/*.cljc"
+        }
     }
 }
diff --git a/src/test/groovy/nebula/plugin/clojure/NoToolchainNebulaClojurePluginIntegrationSpec.groovy b/src/test/groovy/nebula/plugin/clojure/NoToolchainNebulaClojurePluginIntegrationSpec.groovy
index f840e9b..bfb897c 100644
--- a/src/test/groovy/nebula/plugin/clojure/NoToolchainNebulaClojurePluginIntegrationSpec.groovy
+++ b/src/test/groovy/nebula/plugin/clojure/NoToolchainNebulaClojurePluginIntegrationSpec.groovy
@@ -40,6 +40,36 @@ class NoToolchainNebulaClojurePluginIntegrationSpec extends BaseIntegrationTestK
         new File(projectDir, "//build/classes/java/main/test/nebula/app.clj").exists()
     }
 
+    def 'can compile clojure when non-clojure files are present in the source directory'() {
+        buildFile << '''\
+            plugins {
+                id 'com.netflix.nebula.clojure'
+            }
+
+            repositories { mavenCentral() }
+
+            dependencies {
+                implementation 'org.clojure:clojure:1.10.3'
+            }
+            '''.stripIndent()
+
+        settingsFile << 'rootProject.name="can-compile-clojure-with-readme"'
+
+        def clojurefiles = new File(projectDir, 'src/main/clojure/test/nebula')
+        clojurefiles.mkdirs()
+        new File(clojurefiles, 'app.clj').text = APP_CLJ
+        new File(clojurefiles, 'README.md').text = '# Not a clojure file'
+
+        when:
+        def result = runTasks('build', '-s')
+
+        then:
+        noExceptionThrown()
+
+        and:
+        new File(projectDir, "//build/classes/java/main/test/nebula/app.clj").exists()
+    }
+
     def 'can compile clojure with aotCompile'() {
         buildFile << '''\
             plugins {