Fix inclusion bug.

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/FileSpec.kt

@@ -42,9 +42,13 @@ sealed class IFileSpec {
             val includes = Glob(*spec.toTypedArray())
 
             if (File(filePath).isDirectory) {
-                Files.walkFileTree(Paths.get(filePath), object : SimpleFileVisitor<Path>() {
+                val rootDir = if (File(filePath).isAbsolute) Paths.get(filePath)
-                    override public fun visitFile(path: Path, attrs: BasicFileAttributes): FileVisitResult {
+                    else if (baseDir != null) Paths.get(baseDir, filePath)
-                        val rel = Paths.get(filePath).relativize(path)
+                    else Paths.get(filePath)
+                Files.walkFileTree(rootDir, object : SimpleFileVisitor<Path>() {
+                    override fun visitFile(path: Path, attrs: BasicFileAttributes): FileVisitResult {
+                        val rel = if (baseDir != null && !baseDir.isEmpty()) Paths.get(baseDir).relativize(path)
+                            else path
                         if (isIncluded(includes, excludes, path)) {
                             result.add(rel.toFile())
                         }

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/misc/JarUtils.kt

@@ -4,6 +4,7 @@ import com.beust.kobalt.Glob
 import com.beust.kobalt.IFileSpec
 import com.google.common.io.CharStreams
 import java.io.*
+import java.nio.file.Paths
 import java.util.jar.JarEntry
 import java.util.jar.JarFile
 import java.util.jar.JarInputStream
@@ -39,7 +40,7 @@ public class JarUtils {
 
                 // Turn the found file into the local physical file that will be put in the jar file
                 val localFile = if (File(foundFile.path).isAbsolute) File(foundFile.path)
-                    else file.from(foundFile.path)
+                    else File(directory, file.from(foundFile.path).path)
 
                 if (!localFile.exists()) {
                     throw AssertionError("File should exist: $localFile")
@@ -174,7 +175,7 @@ class IncludedFile(val fromOriginal: From, val toOriginal: To, val specs: List<I
                 result.add(if (source.isAbsolute) source else File(source.path))
             }
         }
-        return result
+        return result.map { Paths.get(it.path).normalize().toFile()}
     }
 }
 

src/main/kotlin/com/beust/kobalt/plugin/packaging/JarGenerator.kt

@@ -38,7 +38,7 @@ class JarGenerator @Inject constructor(val dependencyManager: DependencyManager)
             filesNotExcluded.forEach {
                 fileSpecs.add(IFileSpec.FileSpec(it.path.toString().substring(prefixPath.toString().length + 1)))
             }
-            result.add(IncludedFile(From(project.directory + "/" + prefixPath.toString() + "/"), To(""), fileSpecs))
+            result.add(IncludedFile(From(prefixPath.toString()), To(""), fileSpecs))
 
             // Resources, if applicable
             context.variant.resourceDirectories(project).forEach {
@@ -48,7 +48,8 @@ class JarGenerator @Inject constructor(val dependencyManager: DependencyManager)
             //
             // The user specified an include, just use it verbatim
             //
-            result.addAll(PackagingPlugin.findIncludedFiles(project.directory, jar.includedFiles, jar.excludes))
+            val includedFiles = PackagingPlugin.findIncludedFiles(project.directory, jar.includedFiles, jar.excludes)
+            result.addAll(includedFiles)
         }
 
         //

src/main/kotlin/com/beust/kobalt/plugin/packaging/PackagingPlugin.kt

@@ -14,6 +14,7 @@ import com.beust.kobalt.misc.*
 import java.io.File
 import java.io.FileOutputStream
 import java.io.OutputStream
+import java.nio.file.Paths
 import java.util.*
 import java.util.zip.ZipOutputStream
 import javax.inject.Inject
@@ -51,13 +52,14 @@ class PackagingPlugin @Inject constructor(val dependencyManager : DependencyMana
                     val fromPath = includedFile.from
                     if (File(fromPath).exists()) {
                         spec.toFiles(directory, fromPath).forEach { file ->
-                            val fullFile = File(fromPath, file.path)
+                            val fullFile = File(KFiles.joinDir(directory, fromPath, file.path))
                             if (! fullFile.exists()) {
                                 throw AssertionError("File should exist: $fullFile")
                             }
 
                             if (!KFiles.isExcluded(fullFile, excludes)) {
-                                includedSpecs.add(FileSpec(file.path))
+                                val normalized = Paths.get(file.path).normalize().toFile().path
+                                includedSpecs.add(FileSpec(normalized))
                             } else {
                                 log(2, "Not adding ${file.path} to jar file because it's excluded")
                             }

src/test/kotlin/com/beust/kobalt/IncludeExcludeTest.kt

@@ -13,6 +13,7 @@ import java.nio.file.Files
 class IncludeExcludeTest : KobaltTest() {
     private lateinit var topDirectory: File
     private lateinit var directory: File
+    private lateinit var htmlDir: File
 
     val A1 = "A1.class"
     val B1 = "B1.class"
@@ -20,6 +21,7 @@ class IncludeExcludeTest : KobaltTest() {
     val C1 = "C1.class"
     val C2 = "C2.class"
     val C3 = "C3.class"
+    val A_HTML = "a.html"
 
     @BeforeClass
     fun bc() {
@@ -29,26 +31,43 @@ class IncludeExcludeTest : KobaltTest() {
         listOf(A1, B1, B2, C1, C2, C3).forEach {
             File(directory, it).createNewFile()
         }
+
+        htmlDir = Files.createTempDirectory("kobaltTest-").toFile()
+        htmlDir.mkdirs()
+        File(htmlDir, A_HTML).createNewFile()
+    }
+
+    @Test
+    fun html() {
+        val inc = IncludedFile(From(""), To(""), listOf(IFileSpec.GlobSpec("**html")))
+        val files = inc.allFromFiles(htmlDir.path)
+        println("Files " + files)
+        Assert.assertEquals(files.size, 1)
+        Assert.assertEquals(files[0].path, A_HTML)
     }
 
     @DataProvider
     fun dp() : Array<Array<out Any?>> = arrayOf(
-            arrayOf(directory, listOf("A**class", "B**class"), listOf<String>(), listOf(A1, B1, B2)),
+            arrayOf(directory, listOf("**A**class", "**B**class"), listOf<String>(), listOf(A1, B1, B2)),
-            arrayOf(directory, listOf("A**class", "B**class"), listOf("B*class"), listOf(A1)),
+            arrayOf(directory, listOf("**A**class", "**B**class"), listOf("**B*class"), listOf(A1)),
-            arrayOf(directory, listOf("*class"), listOf("B*class"), listOf(A1, C1, C2, C3)),
+            arrayOf(directory, listOf("**class"), listOf("**B*class"), listOf(A1, C1, C2, C3)),
             arrayOf(topDirectory, listOf("**/*class"), listOf<String>(), listOf(A1, B1, B2, C1, C2, C3)),
             arrayOf(topDirectory, listOf("*class"), listOf<String>(), listOf<String>()),
             arrayOf(topDirectory, listOf("**/B*class"), listOf<String>(), listOf(B1, B2)),
-            arrayOf(topDirectory, listOf("**/A*class", "**/B*class"), listOf("B*class"),
+            arrayOf(topDirectory, listOf("**A*class", "**B*class"), listOf("**C*class"),
                     listOf(A1, B1, B2)),
-            arrayOf(topDirectory, listOf("**/A*class", "**/B*class"), listOf("**/B*class"),
+            arrayOf(topDirectory, listOf("**A*class", "**B*class"), listOf("**B*class"),
                 listOf(A1))
     )
 
     @Test(dataProvider = "dp")
-    fun shouldInclude(root: File, includedSpec: List<String>, excludedSpec: List<String>, expectedFiles: List<String>) {
+    fun shouldInclude(root: File, includedSpec: List<String>, excludedSpec: List<String>, expectedFiles:
+    List<String>) {
         val g = IFileSpec.GlobSpec(includedSpec)
-        val files = g.toFiles("", root.path, excludedSpec.map { Glob(it) })
+        val files = g.toFiles(null, root.path, excludedSpec.map { Glob(it) })
+//        if (files.map { it.name } != expectedFiles) {
+//            println("FAILURE")
+//        }
         Assert.assertEquals(files.map { it.name }, expectedFiles)
     }
 

src/test/kotlin/com/beust/kobalt/VerifyKobaltZipTest.kt

@@ -13,7 +13,7 @@ import java.util.jar.JarInputStream
 
 class VerifyKobaltZipTest : KobaltTest() {
     private fun verifyMainJarFile(ins: InputStream) {
-        assertExistsInJarInputStream(JarInputStream(ins), "com/beust/kobalt/MainKt.class", "templates/plugin.jar")
+        assertExistsInJarInputStream(JarInputStream(ins), "com/beust/kobalt/MainKt.class", "templates/kobaltPlugin.jar")
     }
     @Test
     fun verifySourceJarFile() {