Manifold cannot compile or run as "Test Sources"

Describe the bug If the directory that Manifold compiles/runs from is marked as a “Test Sources” folder. You will get a ClassCastException: Error:java: java.lang.ClassCastException: manifold.api.fs.jar.JarEntryFileImpl cannot be cast to manifold.api.fs.jar.JarEntryDirectoryImpl

When used as regular source root folder, compilation/run occurs as normal.

To Reproduce Steps to reproduce the behavior:

1. Create a java class under src/test/java marked as Test Sources Root
2. Utilize manifold (in my case it was with a .JSON manifold in test resources folder)
3. Compile test sources

Expected behavior Class(es) compile/run as they would in regular source root folders.

Screenshots If applicable, add screenshots to help explain your problem (drag/drop them here).

Desktop (please complete the following information):

• OS Type & Version: Mac OS 10.14.5 (18F132)
• Java/JDK version: 8u212
• IntelliJ IDEA version: 2019.1.2
• Manifold version: 0.65
• Manifold IntelliJ plugin version: 0.65

Stack trace

org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:testCompile (default-cli) on project backend: Fatal error compiling
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:212)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
    at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
    at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
    at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
    at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
    at org.codehaus.classworlds.Launcher.main(Launcher.java:47)
Caused by: org.apache.maven.plugin.MojoExecutionException: Fatal error compiling
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:1140)
    at org.apache.maven.plugin.compiler.TestCompilerMojo.execute(TestCompilerMojo.java:181)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
    ... 21 more
Caused by: org.codehaus.plexus.compiler.CompilerException: java.lang.ClassCastException: manifold.api.fs.jar.JarEntryFileImpl cannot be cast to manifold.api.fs.jar.JarEntryDirectoryImpl
    at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:173)
    at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile(JavacCompiler.java:174)
    at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute(AbstractCompilerMojo.java:1129)
    ... 24 more
Caused by: java.lang.RuntimeException: java.lang.ClassCastException: manifold.api.fs.jar.JarEntryFileImpl cannot be cast to manifold.api.fs.jar.JarEntryDirectoryImpl
    at com.sun.tools.javac.main.Main.compile(Main.java:559)
    at com.sun.tools.javac.api.JavacTaskImpl.doCall(JavacTaskImpl.java:129)
    at com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:138)
    at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess(JavaxToolsCompiler.java:126)
    ... 26 more
Caused by: java.lang.ClassCastException: manifold.api.fs.jar.JarEntryFileImpl cannot be cast to manifold.api.fs.jar.JarEntryDirectoryImpl
    at manifold.api.fs.jar.JarEntryDirectoryImpl.getOrCreateDirectory(JarEntryDirectoryImpl.java:43)
    at manifold.api.fs.jar.JarFileDirectoryImpl.processJarEntry(JarFileDirectoryImpl.java:110)
    at manifold.api.fs.jar.JarFileDirectoryImpl.<init>(JarFileDirectoryImpl.ja```

[rsmckinney]

Problem wasn’t so much test v. main sources as it was processing a specific jar file as part of building test sourcers/resources. The sample project you provided (thanks!) has a selenium test dependency jar (I don’t recall the exact name of it) and it had in its META-INF/versions both a directory entry named “9” and a file entry named “9”. My jar file abstraction did not account for this surprise. The fix is available in release 0.68-alpha of both manifold and the ij plugin (plugin available when jetbrains approves the release, probably within a day or two).

[rsmckinney]

Fix available in release 0.68-alpha