First, pick your favorite Javascript based Pretty Print/Beautifier. I prefer the one at http://jsbeautifier.org/, because it's what I found first. Downloads its file https://github.com/beautify-web/js-beautify/blob/master/js/lib/beautify.js

Second, download and install The Mozilla group's Java based Javascript engine, Rhino. "Install" is a little bit misleading; Download the zip file, extract everything, place js.jar in your Java classpath (or Library/Java/Extensions on OS X). You can then run scripts with an invocation similar to this

java -cp js.jar org.mozilla.javascript.tools.shell.Main name-of-script.js

Use the Pretty Print/Beautifier from step 1 to write a small shell script that will read in your javascript file and run it through the Pretty Print/Beautifier from step one. For example

//original code    
(function() { ... js_beautify code ... }());

//new code
print(global.js_beautify(readFile(arguments[0])));

Rhino gives javascript a few extra useful functions that don't necessarily make sense in a browser context, but do in a console context. The function print does what you'd expect, and prints out a string. The function readFile accepts a file path string as an argument and returns the contents of that file.

You'd invoke the above something like

java -cp js.jar org.mozilla.javascript.tools.shell.Main beautify.js file-to-pp.js

You can mix and match Java and Javascript in your Rhino run scripts, so if you know a little Java it shouldn't be too hard to get this running with text-streams as well.

Vim supports formatting source code files with the command gg=G. gg is a (probably redundant) motion that jumps to the beginning of the file; = is the indent command, and the G motion means "execute until end of file". I know, it sounds like alien talk.

In order to execute this on many files, you can create a file and name it whatever you want, e.g. vim-indent.txt, inside which type the following:

gg=G:wq

with a trailing line break.

Basically this file contains a recording of keys we want to press upon running Vim. The :wq<ENTER> command means "write and quit", and it has to be terminated with a line-break. Without that, vim will just type the command and sit there waiting you to press enter manually.

You can then execute the script on a file like this:

vim -s vim-indent.txt your_file.js

The result is that Vim would open the file your_file.js and "press" all keys recorded in vim-indent.txt, the result of which is applying indentation, writing the file and quitting.

You can automate executing this command on an entire file tree using find:

find [path/to/your/directory] -type f -name '*.js' -exec vim -s vim-indent.txt "{}" \;

Note that it's highly recommended that you copy the entire directory, operate on the copy and check whether you like the result.

Check out this post on using JSBeautify with Textmate. It has some good instructions on how to install it on your system. On Mac OS X, I used:

cd /tmp
git clone https://github.com/einars/js-beautify.git
cd js-beautify/python
python setup.py install

Then you can simply use js-beautify /path/to/filename.js to have it run.

However, JS-beautify does work ... in case of all the files in a directory but not in sub-directory

You've mentioned that JS-beautify works if all the input files are in the same directory. Your command doesn't probably work because you pass all the results from find which might include input files from different directories.

As mentioned in the comment earlier, you could use -exec instead:

find . -type f -name "*.html" -exec js-beautify -r {} \;

Newer versions of GNU find might use this syntax:

find . -type f -name "*.html" -exec js-beautify -r {} +