On all Acorn computers fitted with a hard drive, there will be present an application folder named '!Boot'. It is always stored within the root directory - for example, mine is in ADFS::HardDisc4.$ - and, if not present, can cause the machine to fail to boot, or at best be reverted to the stock ROM-only configuration.
Contained within !Boot are quite a few applications and data files, storing the entire system settings for your Archimedes. On later versions of RISC OS 3, double-clicking on !Boot allows you to change these settings from a graphical window - it replaces the near-identical !Configure application's role from earlier versions. If you're feeling adventurous, though, you can manually change all the settings yourself by shift-double clicking !Boot to open the directory in the Filer.
A warning before you even think of poking around with your !Boot files: back it up! Although it is possible to repair some damage done using the !ResetBoot application, it is impossible (or at least, sufficiently difficult) to create a new one if you accidentally delete it. If you keep a backup and you do end up making a mistake, simply delete the damaged one and use the filer to copy your backup back to $.
Ok, now that's out of the way. Shift-double click on !Boot and it'll open up in a filer window (ADFS::HardDisc4.$.!Boot). You should see a number of data files (with type Obey), some sprite files, a couple of text files, and some folders. Within the root of !Boot we find:
!Boot: Yes, within !Boot is an Obey file named !Boot. This sets a number of command-line aliases.
!mine: This shows the Filer a number of applications, so that their filetypes are correctly associated. If you're unable to open a certain type of file without opening its parent application folder first, add that application's path to this file.
!Run: Sets a number of system settings, and loads certain modules (for example, VProtect, if installed)
!Sprites, !Sprites22: These contain the icons shown in Filer windows (a folder with the Archimedes slanted A logo above it)
!Help: This contains the text displayed if one menu-clicks !Boot and chooses 'Help'.
The Choices directory contains two subdirectories: Boot and Printers, the latter of which is (by default) empty. Within Boot:
Desktop: The desktop boot file, which loads applications and Filer windows as specified. (You can create a Desktop boot file by menu-clicking the Task Manager icon on the icon bar)
Predesktop: An Obey file which is Obeyed before the desktop is loaded.
Predesk, Tasks: Two directories containing Obey files, loaded with or before the desktop.
Library contains the FontMerge directory, which itself is Obeyed when a !Fonts application is merged (see below). Within Resources, however, we find:
!ARMovie: A player for Acorn Replay files, not to be confused with the (far better) !ARPlayer.
!Configure*: It's not gone, only hiding. This is run if a user double-clicks on !Boot.
!Fonts: Stores all the system's fonts. Newer !Fonts can be 'merged' with this one through !Configure.
!Scrap: The system scrap file, which is used by applications as temporary storage.
!System: Very important application, containing core and updated modules. New modules can be added using !SysMerge.
Configure: This directory contains numerous settings made via !Configure.
Finally, Utils contains modules, Obeys, Absolutes, and other system-related files.
* Removing !Configure will prevent settings from being changed through running !Boot; double-clicking it will produce an error message stating that the computer's settings may not be changed.
All information taking from my own knowledge and extensive usage of my Acorn A7000. All information applies to RISC OS 3.6; if there are any major differences in other versions, /msg me.