When comparing Caja vs Thunar, the Slant community recommends Thunar for most people. In the question“What are the best Linux file managers?” Thunar is ranked 6th while Caja is ranked 13th. The most important reason people chose Thunar is:
Use Custom Actions to add right-click options to do things like Open as Root, Open Git GUI, etc. You can filter the file types and filename patterns that the actions will show up for. To add an "Open as Root" action, go to Edit, Configure custom actions. Assign a name and a description. Set Command as "gksudo xdg-open %f" (you'll need to install gksudo since pkexec won't work). Pick an icon (I prefer "changes-allow"). Under Appearance Conditions, select Directories, Text Files, and Other Files.
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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 Easy to configure
Pro Custom actions are easy to set up
Use Custom Actions to add right-click options to do things like Open as Root, Open Git GUI, etc. You can filter the file types and filename patterns that the actions will show up for.
To add an "Open as Root" action, go to Edit, Configure custom actions. Assign a name and a description. Set Command as "gksudo xdg-open %f" (you'll need to install gksudo since pkexec won't work). Pick an icon (I prefer "changes-allow"). Under Appearance Conditions, select Directories, Text Files, and Other Files.
Pro Minimal Dependencies
Unlike Nautilus, which requires the whole GNOME desktop, thunar just depends on some XFCE utilities & GTK.
Pro Supports "quick-directory" typing
While in a Thunar window, typing either a "~" or a "/" will automatically start typing into the "address-bar" and pressing enter goes straight to the typed directory.
Use tabs to open fewer windows. New tabs automatically start in the same location. Tabs can be detached.
Pro Non-recursive find
In a thunar window, any non-directory typing will search in the current directory for the filename that you type (non-recursive, unlike Nautilus)
Pro Supports forward/back mouse buttons
Supports the M4 and M5 mouse buttons for forward/back, similarly to most browsers.
Pro Select by Pattern
Select multiple files in the current folder using a wildcard pattern.
Pro Keypress to search in folder
While in a Thunar window, typing a filename automatically selects the first matching file in the current folder.
Pro Supports renaming files in bulk
With also predefined functions as insert (date, numbering,...), search/replace, etc ...
Pro Can assign custom shortcuts to scripts in XFCE
Thunar can use the editable accelerator feature of XFCE.
xfce4-appearance-settings in terminal, go to settings tab, check "enable editable accelerator". Now open any command in Thunar menu, hover to a command, i.e. your custom "places" or your custom command, then press any combination to assign a shortcut to it.
be careful tho, cause it will also remove the shortcut from other command.
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 Tree sidepane missing features
When the sidepane is in Tree mode, it does not show Places (Favorites). It also doesn't collapse folders (like Windows Explorer), adding to clutter.
Con Simplified action bar
The action bar on Thunar is very simple and doesn't have as many features and buttons as other file managers. It only has a back, forward, up, and home buttons as well as the folder path.
Con Requires plugins for some basic functions of modern file managers
Con Requires GNOME dependencies to support common features
Thunar relies on GVFS to support mounting disks or accessing web folders, however since GVFS is a third party GNOME library and made for the use in the GNOME environment its often incompatible to Thunar stable releases which results into crashes and other issues
Con No Split View without a patch, which can be a deal breaker
This limitation can be quite annoying indeed.. thanks for the heads up!
Con Does not integrate well into Gnome
Con Slightly unstable
Thunar crashes some times on file moves, copy-pasting etc. The developers are working on it, but it's taken a while.
Con Image thumbnails sometimes wrong
There seems to be a bug where sometimes images get the wrong thumbnail, this can lead to data-loss.