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Not A Commander is yet another file manager modeled after the Norton Commander. Good integration with the command line is the primary goal.

Tux Commander is a GTK2 file manager with two side-by-side panels.
Some of its functions are inspired by Total Commander. The main goal
of this project is to create a powerful user-friendly file manager for
Linux.

gcp (Goffi's CoPier) is a command line file copying tool, loosely inspired by cp, but with high level functionality like a progress indicator, the ability to continue copying multiple files even when there is a problem with one of them, and the use of a journal to track successful copying. File names can be fixed to ensure compatibility with the target filesystem. If you launch a copy operation when another is already running, the files are added to the first queue to avoid hard drive thrashing. You can keep track of files you have copied, and re-copy them later. gcp is approximately option-compatible with cp.

PhpCommander is a Web-based file manager that manages Web accounts without FTP access. It can create directories, create files, copy, move, delete, and rename files and folders, upload files, download files, view and edit the contents of the files, and communicate in English and other languages.

Xplorer is a file manager with fast and accurate
filetype detection. It has a tree and a list field
displaying the contents of your local filesystem.
Drag and drop, and cut and paste are supported
along with deleting, renaming, and creating files.
It does not have embedded file viewers, but
launches the external applications of your choice.
The package runs directly on Xlib and does not
have a dependency on external toolkits.

GFileRunner is a GNOME file manager aimed to be a
nicer, faster, and more powerful replacement for
the current popular file manager, Nautilus.

4Pane is a four pane detailed-list file manager
for Linux. It is designed to be fully-featured
without bloat, and aims for speed rather than
visual effects. In addition to standard file
manager things, it offers multiple undo and redo
of most operations (including deletions), archive
management including 'virtual browsing' inside
archives, multiple renaming/duplication of files,
a terminal emulator, and user-defined tools.

kfsmd (kernel filesystem monitor daemon) is a
daemon to log and view kernel filesystem changes
using inotify. Its main purpose is to allow
libferris to reindex all updated files while you
are sleeping.

cdargs adds a bookmark feature and a simple filebrowser to the builtin shell command `cd'. This lets you jump to various places throughout the filesystem with just a few keystrokes. It is intended for heavy shell users.

Catharsis.NET.Repository is a library that provides an abstraction over persistent data storages by introducing common repository pattern interfaces over popular ORM frameworks (NHibernate, Entity Framework, LINQ2SQL).

Gfilemanager is a GTK+ 2 filemanager with Samba support.

Find4j is a platform-independent file search tool that can look for files in any hierarchy of filesystem folders or nested zip-compatible archives such a zip, jar, war, ear, and more. It can be used from an intuitive and user-friendly graphical frontend or from the command line.