1 & 2 are simple manual operations of copying the entries from Jar to another adding or leaving the entries you want, deleting he original file and renaming the new to replace it.
As jtahlbom has pointed out, the Java Jar API handles the rest out of the box.
UPDATE with example
These are REALLY basic examples. They show you how to read and write a Jar. Basically from that you can derive just about everything else you need to do.
I've setup a personal library (not included) which basically allows me to pass in an InputStream and have it written to an OutputStream and visa versa. This means you could read from any where and write to anywhere, which could cover most of you requirements.
public void unjar(File jar, File outputPath) throws IOException {
JarFile jarFile = null;
try {
if (outputPath.exits() || outputPathFile.mkdirs()) {
jarFile = new JarFile(jar);
Enumeration<JarEntry> entries = jarFile.entries();
while (entries.hasMoreElements()) {
JarEntry entry = entries.nextElement();
File path = new File(outputPath + File.separator + entry.getName());
if (entry.isDirectory()) {
if (!path.exists() && !path.mkdirs()) {
throw new IOException("Failed to create output path " + path);
}
} else {
System.out.println("Extracting " + path);
InputStream is = null;
OutputStream os = null;
try {
is = jarFile.getInputStream(entry);
os = new FileOutputStream(path);
byte[] byteBuffer = new byte[1024];
int bytesRead = -1;
while ((bytesRead = is.read(byteBuffer)) != -1) {
os.write(byteBuffer, 0, bytesRead);
}
os.flush();
} finally {
try {
os.close();
} catch (Exception e) {
}
try {
is.close();
} catch (Exception e) {
}
}
}
}
} else {
throw IOException("Output path does not exist/could not be created");
}
} finally {
try {
jarFile.close();
} catch (Exception e) {
}
}
}
public void jar(File jar, File sourcePath) throws IOException {
JarOutputStream jos = null;
try {
jos = new JarOutputStream(new FileOutputStream(jar));
List<File> fileList = getFiles(sourcePath);
System.out.println("Jaring " + fileList.size() + " files");
List<String> lstPaths = new ArrayList<String>(25);
for (File file : fileList) {
String path = file.getParent().replace("\\", "/");
String name = file.getName();
path = path.substring(sourcePath.getPath().length());
if (path.startsWith("/")) {
path = path.substring(1);
}
if (path.length() > 0) {
path += "/";
if (!lstPaths.contains(path)) {
JarEntry entry = new JarEntry(path);
jos.putNextEntry(entry);
jos.closeEntry();
lstPaths.add(path);
}
}
System.out.println("Adding " + path + name);
JarEntry entry = new JarEntry(path + name);
jos.putNextEntry(entry);
FileInputStream fis = null;
try {
fis = new FileInputStream(file);
byte[] byteBuffer = new byte[1024];
int bytesRead = -1;
while ((bytesRead = fis.read(byteBuffer)) != -1) {
jos.write(byteBuffer, 0, bytesRead);
}
jos.flush();
} finally {
try {
fis.close();
} catch (Exception e) {
}
}
jos.closeEntry();
}
jos.flush();
} finally {
try {
jos.close();
} catch (Exception e) {
}
}
}
If you take the time look, there are a number of examples of how to add/remove entries from the from zip/jar files on SO
