Bug fix for new --run flag (#1068)

* Ensure that CPG is written to disk in `runBundle`

* Introduce `--store` flag

* Tell user where the logs are in `--run` executions

Author: fabsx00

console/src/main/scala/io/shiftleft/console/BridgeBase.scala

@@ -19,6 +19,7 @@ case class Config(
     src: Option[String] = None,
     language: Option[String] = None,
     overwrite: Boolean = false,
+    store: Boolean = false,
     server: Boolean = false,
     serverHost: String = "localhost",
     serverPort: Int = 8080,
@@ -85,6 +86,10 @@ trait BridgeBase {
         .action((_, c) => c.copy(overwrite = true))
         .text("Overwrite CPG if it already exists")
 
+      opt[Unit]("store")
+        .action((_, c) => c.copy(store = true))
+        .text("Store graph changes made by bundle")
+
       note("REST server mode")
 
       opt[Unit]("server")
@@ -188,19 +193,24 @@ trait BridgeBase {
     val bundleName = config.bundleToRun.get
     val src = config.src.get
     val language = config.language.getOrElse("c")
+    val storeCode = if (config.store) { "save" } else { "" }
     val code = s"""
         | if (${config.overwrite} || !workspace.projectExists("$src")) {
         |   importCode.$language("$src")
+        |   save
         | } else {
         |    println("Using existing CPG - Use `--overwrite` if this is not what you want")
         |    workspace.projects
         |    .filter(x => x.inputPath == better.files.File("$src").path.toAbsolutePath.toString)
         |    .map(_.name).map(open)
         | }
         | run.$bundleName
+        | $storeCode
         |""".stripMargin
 
-    val file = new java.io.File("run-log.txt");
+    val logFileName = "run-log.txt"
+    println(s"Detailed logs at: $logFileName")
+    val file = new java.io.File(logFileName);
     val fos = new FileOutputStream(file);
     val ps = new PrintStream(fos);
     System.setErr(ps)