I'm curious, what phone do you use?
Browse the file system? Very easy. There are many free and paid file managers. You can also use a terminal emulator.
Obtain root access? OEM unlock bootloader, throw su on the phone and you are set.
Recompile and update the kernel? I has never built my own kernel, but there are many custom kernels popping up all the time.
Replace the window manager? To change the desktop environment, most people just install a different "launcher". That changes how the desktop, windowing, and general interface operate. If you really wanted to have the full freedom of Linux, you can install something like Debian on an android device with a dual boot setup or run it on top of android through a VNC client.
I would prefer a fully free software stack, but I realize that that's not always possible, so I like to support the next best thing. Traditional consoles have always been so hacking unfriendly that I have refused to buy them.
Just so you know, a Nexus One was the first cell phone I ever bought; it was the first that I considered free enough (and capable enough; the Dream/G1 was just a little too clunky for me to consider it particularly useful).