(Build) Fixed directory problems for edg-generate-sig

The script assumed that the build directory was somewhere
inside the source tree.
(Java) Install all Java files to eliminate JVM crash

We need to install all of the Java build products
in $ROSE[_BUILD]/src/3rdPartyLibraries/java-parser
otherwise ROSE won't be able to find our classes.

Particularly, `jserver_FindClass("JavaTraversal")`
returns NULL because the class is not loaded in
the JVM within the ECJ-ROSE Connection.

The installed ROSE translator uses this classpath:

    -Djava.class.path=
    $ROSE_INSTALL/lib/antlr-3.3-complete.jar
    $ROSE_INSTALL/lib/OpenFortranParser-20111001.jar
    $ROSE_INSTALL/lib/ecjROSE.jar
    $ROSE_INSTALL/lib/

Before this patch, `ecjROSE.jar` and all of the
`java-parser/*class` files were missing.
Particularly, `JavaTraversal.class` was missing.
Installing all of these files resolves this issue.

(TODO) Will be added in future commit
As a precautionary measure, we need to add some
assertions in ecj.C to ensure that the
"JavaTraversal" class is found successfully. An
assertion is a lot more friendly and useful than
a JVM crash report.

```C++
static int jofp_invoke(int argc, char **argv) {
+    if (argc > 0) {
+        assert(argv != NULL);
+    }

...

-    // tps : this code is more transparent and easier to read
+    // TOO1 (12/5/2012) - In order for the "JavaTraversal" class to be found,
+    //                    it must have been loaded into the JVM, i.e. the file
+    //                    "JavaTraversal.class" must be in the classpath.
     jclass cls = jserver_FindClass("JavaTraversal");
+    assert(cls != NULL);
```