diff --git a/src/main/kotlin/com/beust/kobalt/internal/build/BuildFile.kt b/src/main/kotlin/com/beust/kobalt/internal/build/BuildFile.kt
new file mode 100644
index 00000000..17954ed0
--- /dev/null
+++ b/src/main/kotlin/com/beust/kobalt/internal/build/BuildFile.kt
@@ -0,0 +1,17 @@
+package com.beust.kobalt.internal.build
+
+import java.io.File
+import java.nio.file.Files
+import java.nio.file.Path
+import java.nio.file.attribute.BasicFileAttributes
+/**
+ * Sometimes, build files are moved to temporary files, so we give them a specific name for clarity.
+ */
+class BuildFile(val path: Path, val name: String) {
+    public fun exists() : Boolean = Files.exists(path)
+
+    public val lastModified : Long
+        get() = Files.readAttributes(path, BasicFileAttributes::class.java).lastModifiedTime().toMillis()
+
+    public val directory : File get() = path.toFile().directory
+}
diff --git a/src/main/kotlin/com/beust/kobalt/internal/build/BuildFileCompiler.kt b/src/main/kotlin/com/beust/kobalt/internal/build/BuildFileCompiler.kt
new file mode 100644
index 00000000..41ce498d
--- /dev/null
+++ b/src/main/kotlin/com/beust/kobalt/internal/build/BuildFileCompiler.kt
@@ -0,0 +1,126 @@
+package com.beust.kobalt.internal.build
+
+import com.beust.kobalt.Args
+import com.beust.kobalt.KobaltException
+import com.beust.kobalt.Plugins
+import com.beust.kobalt.api.Kobalt
+import com.beust.kobalt.api.KobaltContext
+import com.beust.kobalt.api.PluginProperties
+import com.beust.kobalt.api.Project
+import com.beust.kobalt.internal.PluginInfo
+import com.beust.kobalt.internal.build.VersionFile
+import com.beust.kobalt.maven.DependencyManager
+import com.beust.kobalt.misc.KFiles
+import com.beust.kobalt.misc.KobaltExecutors
+import com.beust.kobalt.misc.log
+import com.beust.kobalt.plugin.kotlin.kotlinCompilePrivate
+import com.google.inject.assistedinject.Assisted
+import rx.subjects.PublishSubject
+import java.io.File
+import java.net.URL
+import java.nio.file.Paths
+import javax.inject.Inject
+
+/**
+ * Manage the compilation of Build.kt. There are two passes for this processing:
+ * 1) Extract the repos() and plugins() statements in a separate .kt and compile it into preBuildScript.jar.
+ * 2) Actually build the whole Build.kt file after adding to the classpath whatever phase 1 found (plugins, repos)
+ */
+public class BuildFileCompiler @Inject constructor(@Assisted("buildFiles") val buildFiles: List<BuildFile>,
+        @Assisted val pluginInfo: PluginInfo, val files: KFiles, val plugins: Plugins,
+        val dependencyManager: DependencyManager, val pluginProperties: PluginProperties,
+        val executors: KobaltExecutors, val buildScriptUtil: BuildScriptUtil) {
+
+    interface IFactory {
+        fun create(@Assisted("buildFiles") buildFiles: List<BuildFile>, pluginInfo: PluginInfo) : BuildFileCompiler
+    }
+
+    val observable = PublishSubject.create<List<Project>>()
+
+    private val SCRIPT_JAR = "buildScript.jar"
+
+    fun compileBuildFiles(args: Args): List<Project> {
+        //
+        // Create the KobaltContext
+        //
+        val context = KobaltContext(args)
+        context.pluginInfo = pluginInfo
+        context.pluginProperties = pluginProperties
+        context.dependencyManager = dependencyManager
+        context.executors = executors
+        Kobalt.context = context
+
+        //
+        // Find all the projects in the build file, possibly compiling them
+        //
+        val allProjects = findProjects(context)
+        plugins.applyPlugins(context, allProjects)
+
+        return allProjects
+    }
+
+    private fun findProjects(context: KobaltContext): List<Project> {
+        val result = arrayListOf<Project>()
+        buildFiles.forEach { buildFile ->
+            val processBuildFile = parseBuildFile(context, buildFile)
+            val pluginUrls = processBuildFile.pluginUrls
+            val buildScriptJarFile = File(KFiles.findBuildScriptLocation(buildFile, SCRIPT_JAR))
+
+            // If the script jar files were generated by a different version, wipe them in case the API
+            // changed in-between
+            buildScriptJarFile.parentFile.let { dir ->
+                if (! VersionFile.isSameVersionFile(dir)) {
+                    log(1, "Detected new installation, wiping $dir")
+                    dir.listFiles().map { it.delete() }
+                }
+            }
+
+            // Write the modified Build.kt (e.g. maybe profiles were applied) to a temporary file,
+            // compile it, jar it in buildScript.jar and run it
+            val modifiedBuildFile = KFiles.createTempFile(".kt")
+            KFiles.saveFile(modifiedBuildFile, processBuildFile.buildScriptCode)
+            maybeCompileBuildFile(context, BuildFile(Paths.get(modifiedBuildFile.path), "Modified Build.kt"),
+                    buildScriptJarFile, pluginUrls)
+            val projects = buildScriptUtil.runBuildScriptJarFile(buildScriptJarFile, pluginUrls, context)
+            result.addAll(projects)
+        }
+        return result
+    }
+
+    private fun maybeCompileBuildFile(context: KobaltContext, buildFile: BuildFile, buildScriptJarFile: File,
+            pluginUrls: List<URL>) {
+        log(2, "Running build file ${buildFile.name} jar: $buildScriptJarFile")
+
+        if (buildScriptUtil.isUpToDate(buildFile, buildScriptJarFile)) {
+            log(2, "Build file is up to date")
+        } else {
+            log(2, "Need to recompile ${buildFile.name}")
+
+            buildScriptJarFile.delete()
+            kotlinCompilePrivate {
+                classpath(files.kobaltJar)
+                classpath(pluginUrls.map { it.file })
+                sourceFiles(listOf(buildFile.path.toFile().absolutePath))
+                output = buildScriptJarFile
+            }.compile(context = context)
+
+            if (! buildScriptJarFile.exists()) {
+                throw KobaltException("Could not compile ${buildFile.name}")
+            }
+        }
+    }
+
+    /**
+     * Generate the script file with only the plugins()/repos() directives and run it. Then return
+     * - the source code for the modified Build.kt (after profiles are applied)
+     * - the URL's of all the plug-ins that were found.
+     */
+    private fun parseBuildFile(context: KobaltContext, buildFile: BuildFile) : ParsedBuildFile {
+        // Parse the build file so we can generate preBuildScript and buildScript from it.
+        with(ParsedBuildFile(buildFile, context, buildScriptUtil, dependencyManager, files)) {
+            // Notify possible listeners (e.g. KobaltServer) we now have all the projects
+            observable.onNext(projects)
+            return this
+        }
+    }
+}
diff --git a/src/main/kotlin/com/beust/kobalt/internal/build/BuildScriptUtil.kt b/src/main/kotlin/com/beust/kobalt/internal/build/BuildScriptUtil.kt
new file mode 100644
index 00000000..7fceb1a9
--- /dev/null
+++ b/src/main/kotlin/com/beust/kobalt/internal/build/BuildScriptUtil.kt
@@ -0,0 +1,135 @@
+package com.beust.kobalt.internal.build
+
+import com.beust.kobalt.KobaltException
+import com.beust.kobalt.Plugins
+import com.beust.kobalt.api.IPlugin
+import com.beust.kobalt.api.KobaltContext
+import com.beust.kobalt.api.Project
+import com.beust.kobalt.api.annotation.Task
+import com.beust.kobalt.internal.build.BuildFile
+import com.beust.kobalt.misc.KFiles
+import com.beust.kobalt.misc.Topological
+import com.beust.kobalt.misc.log
+import com.google.inject.Inject
+import java.io.File
+import java.io.FileInputStream
+import java.io.InputStream
+import java.lang.reflect.Modifier
+import java.net.URL
+import java.net.URLClassLoader
+import java.util.*
+import java.util.jar.JarInputStream
+
+class BuildScriptUtil @Inject constructor(val plugins: Plugins, val files: KFiles){
+    val projects = arrayListOf<Project>()
+
+    /**
+     * Run the given preBuildScript (or buildScript) jar file, using a classloader made of the passed URL's.
+     * This list is empty when we run preBuildScript.jar but for buildScript.jar, it contains the list of
+     * URL's found from running preBuildScript.jar.
+     */
+    fun runBuildScriptJarFile(buildScriptJarFile: File, urls: List<URL>,
+            context: KobaltContext) : List<Project> {
+        var stream : InputStream? = null
+        val allUrls = (urls + arrayOf(
+                buildScriptJarFile.toURI().toURL()) + File(files.kobaltJar).toURI().toURL())
+                .toTypedArray()
+        val classLoader = URLClassLoader(allUrls)
+
+        //
+        // Install all the plugins
+        //
+        plugins.installPlugins(Plugins.dynamicPlugins, classLoader)
+
+        //
+        // Classload all the jar files and invoke their methods
+        //
+        try {
+            stream = JarInputStream(FileInputStream(buildScriptJarFile))
+            var entry = stream.nextJarEntry
+
+            val classes = hashSetOf<Class<*>>()
+            while (entry != null) {
+                val name = entry.name;
+                if (name.endsWith(".class")) {
+                    val className = name.substring(0, name.length - 6).replace("/", ".")
+                    var cl : Class<*>? = classLoader.loadClass(className)
+                    if (cl != null) {
+                        classes.add(cl)
+                    } else {
+                        throw KobaltException("Couldn't instantiate $className")
+                    }
+                }
+                entry = stream.nextJarEntry;
+            }
+
+            // Invoke all the "val" found on the _DefaultPackage class (the Build.kt file)
+            classes.filter { cls ->
+                cls.name != "_DefaultPackage"
+            }.forEach { cls ->
+                cls.methods.forEach { method ->
+                    // Invoke vals and see if they return a Project
+                    if (method.name.startsWith("get") && Modifier.isStatic(method.modifiers)) {
+                        try {
+                            val r = method.invoke(null)
+                            if (r is Project) {
+                                log(2, "Found project $r in class $cls")
+                                projects.add(r)
+                            }
+                        } catch(ex: Throwable) {
+                            throw ex.cause ?: KobaltException(ex)
+                        }
+                    } else {
+                        val taskAnnotation = method.getAnnotation(Task::class.java)
+                        if (taskAnnotation != null) {
+                            Plugins.defaultPlugin.methodTasks.add(IPlugin.MethodTask(method, taskAnnotation))
+                        }
+
+                    }}
+            }
+        } finally {
+            stream?.close()
+        }
+
+        validateProjects(projects)
+
+        //
+        // Now that the build file has run, fetch all the project contributors, grab the projects from them and sort
+        // them topologically
+        //
+        Topological<Project>().let { topologicalProjects ->
+            val all = hashSetOf<Project>()
+            context.pluginInfo.projectContributors.forEach { contributor ->
+                val descriptions = contributor.projects()
+                descriptions.forEach { pd ->
+                    all.add(pd.project)
+                    pd.dependsOn.forEach { dependsOn ->
+                        topologicalProjects.addEdge(pd.project, dependsOn)
+                        all.add(dependsOn)
+                    }
+                }
+            }
+            val result = topologicalProjects.sort(ArrayList(all))
+
+            return result
+        }
+    }
+
+    fun isUpToDate(buildFile: BuildFile, jarFile: File) =
+            buildFile.exists() && jarFile.exists()
+                    && buildFile.lastModified < jarFile.lastModified()
+
+    /**
+     * Make sure all the projects have a unique name.
+     */
+    private fun validateProjects(projects: List<Project>) {
+        val seen = hashSetOf<String>()
+        projects.forEach {
+            if (seen.contains(it.name)) {
+                throw KobaltException("Duplicate project name: $it")
+            } else {
+                seen.add(it.name)
+            }
+        }
+    }
+}
diff --git a/src/main/kotlin/com/beust/kobalt/internal/build/ParsedBuildFile.kt b/src/main/kotlin/com/beust/kobalt/internal/build/ParsedBuildFile.kt
new file mode 100644
index 00000000..7e6df00d
--- /dev/null
+++ b/src/main/kotlin/com/beust/kobalt/internal/build/ParsedBuildFile.kt
@@ -0,0 +1,133 @@
+package com.beust.kobalt.internal.build
+
+import com.beust.kobalt.Plugins
+import com.beust.kobalt.api.KobaltContext
+import com.beust.kobalt.api.Project
+import com.beust.kobalt.internal.build.VersionFile
+import com.beust.kobalt.internal.build.BuildFile
+import com.beust.kobalt.internal.build.BuildScriptUtil
+import com.beust.kobalt.maven.DependencyManager
+import com.beust.kobalt.misc.KFiles
+import com.beust.kobalt.misc.countChar
+import com.beust.kobalt.misc.log
+import com.beust.kobalt.plugin.kotlin.kotlinCompilePrivate
+import java.io.File
+import java.net.URL
+import java.nio.charset.Charset
+import java.nio.file.Paths
+import java.util.*
+import kotlin.text.Regex
+
+class ParsedBuildFile(val buildFile: BuildFile, val context: KobaltContext, val buildScriptUtil: BuildScriptUtil,
+        val dependencyManager: DependencyManager, val files: KFiles) {
+    val pluginList = arrayListOf<String>()
+    val repos = arrayListOf<String>()
+    val profileLines = arrayListOf<String>()
+    val pluginUrls = arrayListOf<URL>()
+    val projects = arrayListOf<Project>()
+
+    private val preBuildScript = arrayListOf(
+            "import com.beust.kobalt.*",
+            "import com.beust.kobalt.api.*")
+    val preBuildScriptCode : String get() = preBuildScript.joinToString("\n")
+
+    private val buildScript = arrayListOf<String>()
+    val buildScriptCode : String get() = buildScript.joinToString("\n")
+
+    init {
+        parseBuildFile()
+        initPluginUrls()
+    }
+
+    private fun parseBuildFile() {
+        var parenCount = 0
+        buildFile.path.toFile().forEachLine(Charset.defaultCharset()) { line ->
+            var current: ArrayList<String>? = null
+            var index = line.indexOf("plugins(")
+            if (index >= 0) {
+                current = pluginList
+            } else {
+                index = line.indexOf("repos(")
+                if (index >= 0) {
+                    current = repos
+                }
+            }
+            if (parenCount > 0 || current != null) {
+                if (index == -1) index = 0
+                with(line.substring(index)) {
+                    parenCount += line countChar '('
+                    if (parenCount > 0) {
+                        current!!.add(line)
+                    }
+                    parenCount -= line countChar ')'
+                }
+            }
+
+            /**
+             * If the current line matches one of the profile, turns the declaration into
+             * val profile = true, otherwise return the same line
+             */
+            fun correctProfileLine(line: String) : String {
+                context.profiles.forEach {
+                    if (line.matches(Regex("[ \\t]*val[ \\t]+$it[ \\t]+=.*"))) {
+                        with("val $it = true") {
+                            profileLines.add(this)
+                            return this
+                        }
+                    }
+                }
+                return line
+            }
+
+            buildScript.add(correctProfileLine(line))
+        }
+
+        repos.forEach { preBuildScript.add(it) }
+        pluginList.forEach { preBuildScript.add(it) }
+    }
+
+    private fun initPluginUrls() {
+        //
+        // Compile and run preBuildScriptCode, which contains all the plugins() calls extracted. This
+        // will add all the dynamic plugins found in this code to Plugins.dynamicPlugins
+        //
+        val pluginSourceFile = KFiles.createTempFile(".kt")
+        pluginSourceFile.writeText(preBuildScriptCode, Charset.defaultCharset())
+        log(2, "Saved ${pluginSourceFile.absolutePath}")
+
+        //
+        // Compile to preBuildScript.jar
+        //
+        val buildScriptJar = KFiles.findBuildScriptLocation(buildFile, "preBuildScript.jar")
+        val buildScriptJarFile = File(buildScriptJar)
+        if (! buildScriptUtil.isUpToDate(buildFile, File(buildScriptJar))) {
+            buildScriptJarFile.parentFile.mkdirs()
+            generateJarFile(context, BuildFile(Paths.get(pluginSourceFile.path), "Plugins"), buildScriptJarFile)
+            VersionFile.generateVersionFile(buildScriptJarFile.parentFile)
+        }
+
+        //
+        // Run preBuildScript.jar to initialize plugins and repos
+        //
+        projects.addAll(buildScriptUtil.runBuildScriptJarFile(buildScriptJarFile, arrayListOf<URL>(), context))
+
+        //
+        // All the plug-ins are now in Plugins.dynamicPlugins, download them if they're not already
+        //
+        Plugins.dynamicPlugins.forEach {
+            pluginUrls.add(it.jarFile.get().toURI().toURL())
+        }
+    }
+
+    private fun generateJarFile(context: KobaltContext, buildFile: BuildFile, buildScriptJarFile: File) {
+        val kotlintDeps = dependencyManager.calculateDependencies(null, context)
+        val deps: List<String> = kotlintDeps.map { it.jarFile.get().absolutePath }
+        kotlinCompilePrivate {
+            classpath(files.kobaltJar)
+            classpath(deps)
+            sourceFiles(buildFile.path.toFile().absolutePath)
+            output = File(buildScriptJarFile.absolutePath)
+        }.compile(context = context)
+    }
+}
+
diff --git a/src/main/kotlin/com/beust/kobalt/internal/build/VersionFile.kt b/src/main/kotlin/com/beust/kobalt/internal/build/VersionFile.kt
new file mode 100644
index 00000000..4343ed3f
--- /dev/null
+++ b/src/main/kotlin/com/beust/kobalt/internal/build/VersionFile.kt
@@ -0,0 +1,20 @@
+package com.beust.kobalt.internal.build
+
+import com.beust.kobalt.api.Kobalt
+import com.beust.kobalt.misc.KFiles
+import java.io.File
+
+class VersionFile {
+    companion object {
+        private val VERSION_FILE = "version.txt"
+
+        fun generateVersionFile(directory: File) {
+            KFiles.saveFile(File(directory, VERSION_FILE), Kobalt.version)
+        }
+
+        fun isSameVersionFile(directory: File) =
+            with(File(directory, VERSION_FILE)) {
+                ! exists() || (exists() && readText() == Kobalt.version)
+            }
+    }
+}
\ No newline at end of file