Looks like you're on Windows, so your FileInputStream(SOURCE_FOLDER + File.separator + "META-INF\\container.xml");
statement is correct for the OS, but I'd guess you need to change the other 2 strings to use the forward slash for the zipentry path.
ZipEntry container = new ZipEntry("META-INF\\container.xml");
try instead as
ZipEntry container = new ZipEntry("META-INF/container.xml");
and change
if(!file.toString().equals("mimetype") && !file.toString().equals("META-INF\\container.xml")){
to
if(!file.toString().equals("mimetype") && !file.toString().equals("META-INF/container.xml")){
accordingly.
You may need to adjust your other ZipEntry
's as well. From the ZIP spec (section "4.4.17 file name"):
All slashes MUST be forward slashes '/' as opposed to backwards slashes '\'