When comparing jFileProcessor vs Caja, the Slant community recommends Caja for most people. In the question“What are the best file managers for UNIX-like systems?” Caja is ranked 16th while jFileProcessor is ranked 26th.
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Pros
Pro Easy to run commands on selected files
Find/select files in sub-folders. run touch %f or cp %f /somefolder (this is a way to copy selected files in different levels, into 1 folder, flattening out the copy).
Pro Easy rename files script
Select files. regex to match pieces of filenames, rename adding, leaving out, and reusing saved pieces.
Pro Groovy scripts to watch and act on files that get created/put into a folder.
So you can watch a folder and process files that come into it.
Pro You can make your own file associations. You can make 3 types, per suffix, per filename, per exact file.
With exact file you can create a folder of job or desktop icon names. Double-click that file to run the job since it is tied to just that specific file.
Pro Can make sftp connections
Pro You can write a script to modify your list
Your script can modify contents in the list window it is working on.
Pro Plugin scripts
Just put groovy scripts in menu-scripts folder and they will automatically run using currently selected files.
Pro Run any groovy scriptable command on a list
Run commands on your lists: grep files to find stuff, delete/copy/move files, etc.. Even copy a file to a remote host and execute it.
Pro Create and work with lists of filenames or any string
Search files and save to another file or a list window. Add or subtract one list from another.
Pro Can do count only
Just count matching search criterion.
Pro Good search
Search on modified time, file size, glob/regex name, folder depth; and/or on these and can do range.
Pro Cross-platform
Available for Linux, Windows, macOS - just needs java 7+ (written with 8).
Pro Easy to configure
Pro It has a reasonable set of features, out of the box
Not too much cluttered, but enough customizable.
Pro Caja script extension makes it more useful
Caja script extension adds your script in script menu, then passes the file name as a parameter. This allows you to run operation which is not included in Caja.
Pro Allows you to access remote or local locations
You can click the Files entry in the panel to access a specific location (remote or local), connect to a certain server (FTP, SFTP, SAMBA, etc.), access your bookmarks, open a new window, as well as to change its default functionality.
Pro Open or run as administrator in the right-click-menu of the mouse
Pro It just works
Customizable and clean, this is crushing that garbage nautilus, the overrated p.o.s. gnome destroyed.
Cons
Con Does not see attached phone files
No mtp:/ connected phone files.
Con Frequently very slow to transfer multiple small files
Folders move fine, but it chokes on files, where other browsers take seconds.
Con Mostly unconfigurable
There are not many ways to configure Caja to fit your needs. Besides what can be seen in the settings button you can't configure it further.
Con Sort Order / Limited Configuration Options
It ignores special characters when sorting files and folders. Underscore, tilde, bracket, ASCII characters, .... everthing not recognized in numeric/alpha sorting. Also, I found no way to remove the triangle to reveal contents of sub-folders rather than opening... but I did quit looking after several seemly unalterable functionality issues.
Con Very slow to list thousands of files
Unusably so.