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1 - what files controls what starts up in KDE or in GNOME?
2 - when using the command prompt (xterm), what files controls the paths that you want to use when type a command in xterm. I am tired of having to type the path everytime I want to use a command
It depends on how you are invoking the terminal and with what application. For Konsole on the KDE desktop, you can go to Settings > Session > <session you use> and where it says execute in the window, type in "bash -l." Bash will see what user is logged in as and then emulate their profile, just as if you logged in from console. I know this is very specific but its a start. If you are invoking xterm directly you can pass the "ls" parameter (eg. xterm -ls) and it will do the same thing.
In every user directory there is a hidden KDE config directory called ".kde" (go figure .) Within that directory is another directory called Autostart. On my system, I have my xscreensaver.desktop shortcut placed in there so it will use a screensaver other than the KDE one. Besides Autostart is another directory called "share" and within that folder is another one called "config." Just check it out and you will get the idea. It has config files for Konsole, the desktop, mail, hotkeys, etc...
In regards to default GUI for X, you can put your preferences in your home directory file .xinitrc. When you run "startx", it will run this config file. I am not too familiar with how FC sets up this file but the meat of it is that at the end it will say "exec <window manager>." Just substitue the window manager with the executable for the GUI of choice (eg. kde, fluxbox, gnome.) Run "man startx" to get more detailed information about this.
I am using FC5 and SUSE 10 and there is no .xinitrc profile under my ~/ directory. Where else might it be?
Also I figured out my second question: vim ~/home directory/bash_profile and add the path of the executables that you want and the run source ~/home directory and rock on.
Try creating your own .xinitrc and adding the exec <window manager> statement. Also check out 'man startx' to get distro specific information for starting X. Let me know how it works out?
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