How do I programmatically change file permissions?

Full control over file attributes is available in Java 7, as part of the "new" New IO facility (NIO.2). For example, POSIX permissions can be set on an existing file with setPosixFilePermissions(), or atomically at file creation with methods like createFile() or newByteChannel().

You can create a set of permissions using EnumSet.of(), but the helper method PosixFilePermissions.fromString() will uses a conventional format that will be more readable to many developers. For APIs that accept a FileAttribute, you can wrap the set of permissions with with PosixFilePermissions.asFileAttribute().

Set<PosixFilePermission> ownerWritable = PosixFilePermissions.fromString("rw-r--r--");
FileAttribute<?> permissions = PosixFilePermissions.asFileAttribute(ownerWritable);
Files.createFile(path, permissions);

In earlier versions of Java, using native code of your own, or exec-ing command-line utilities are common approaches.

In addition to erickson's suggestions, there's also jna, which allows you to call native libraries without using jni. It's shockingly easy to use, and I've used it on a couple of projects with great success.

The only caveat is that it's slower than jni, so if you're doing this to a very large number of files that might be an issue for you.

(Editing to add example)

Here's a complete jna chmod example:

import com.sun.jna.Library;
import com.sun.jna.Native;

public class Main {
    private static CLibrary libc = (CLibrary) Native.loadLibrary("c", CLibrary.class);

    public static void main(String[] args) {
        libc.chmod("/path/to/file", 0755);
    }
}

interface CLibrary extends Library {
    public int chmod(String path, int mode);
}