When comparing Caja vs SpaceFM, the Slant community recommends SpaceFM for most people. In the question“What are the best file managers for UNIX-like systems?” SpaceFM is ranked 11th while Caja is ranked 16th. The most important reason people chose SpaceFM is:
Just right click on any menu or menu option (including the context menu itself) and you'll be allowed to customize it. This lets you add support or integration for features you find missing.
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Pros
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.
Pro Incredibly customizable
Just right click on any menu or menu option (including the context menu itself) and you'll be allowed to customize it. This lets you add support or integration for features you find missing.
Pro Minimal dependencies
It only needss gtk, udev, desktop-file-util and shared-mime-info which is available in most systems.
Pro Highly extensible
Functionalities can be extended by user scripts as plugins. Some scripts can also be downloaded from https://github.com/IgnorantGuru/spacefm-plugins/wiki. Plugins can be exported too.
Pro Tab and panel support
SpaceFM supports up to 4 individually customizable panels as well as multi-tabbed file management.
Pro No back seat driver
Does not obstruct professional work by engrossing root warnings.
Pro Desktop management support
Can be used to set wallpaper and desktop icons with high configuration support.
Pro Easily open folder as root
Can open different folders as root, this way you don't have to use the terminal to move around files for which you need root permission.
Pro Gtk-2 and 3 support
Available in gtk2 and gtk3.
Pro Intuitive and extendable through plug-ins
Great UI, easy to use and configure, several plug-ins available to make everyday tasks even easier.
Cons
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.
Con Ugly
Con Some operations are slow
Because it tries to be as lightweight as possible and tries to use very little RAM. This can unfortunately lead to it being slow sometimes.