Answers to the questions on SO and askubuntu, along with poking through (and reading headers of) $HOME and /etc/, indicate a number of files that can be used to set environment variables, including:~/.profile ~/.bashrc ~/.bash_profile ~/.gnomerc~/.Rprofile /etc/bash_bashrc /etc/profile/etc/screenrc I gather that files in /etc/ work for all users whereas files in $HOME are user-specific. I also gather that .profile is loaded at login whereas .bashrc loaded when /bin/bash is executed. I also understand that different programs have different settings files (e.g. .Rprofile for R). But I would appreciate some clarification:Are *rc and *profile files fundamentally different?What is the scope of such files (e.g. which files are are commonly used with Linux)Is there a hierarchy (e.g. .bashrc overwrites variables set in .settings)What is a good reference for this class of files? For the options in these files?Linked questionsHow to access a bash environment variable from within R in emacs-ess?Difference between launching an application from a keyboard shortcut vs the terminal?
What is the difference between ~/.profile, ~/.bashrc, ~/.bash_profile, ~/.gnomerc, /etc/bash_bashrc, /etc/screenrc ...?
bash;environment variables;profile;settings;bashrc
The organization of configuration files is much less uniform than your questions seem to imply.  There is no class, there is no hierarchy, and there is no global configuration czar nor committee that decrees a common syntax or other nice clean generalizations like the ones you are seeking.  There is only a multitude of separate applications like R, bash, screen and the GNOME desktop environment, all of whom have their own ways of doing things, so you should look at the documentation for each  individual program to answer any specific questions about a particular file.  If it seems ad-hoc, that's because it is: most of Unix / Linux software out there was developed for different purposes by different people who all went about configuration slightly differently.To answer your other questions pointwise:*rc and *profile do not mean very much, so this question can't really be answered.  rc is merely a commonly used abbreviation or suffix for configuration files.  Its etymology goes back to ancient times (in computer years), and probably means run commands (from runcom).  Just because applications use the same word does not mean they agree on conventions.  profile is a much less common suffix.Define scope.  Most applications do not share configuration files with other non-related applications.  The one possible exception is /etc/profile and .profile, which may be used by multiple different shells (including at least sh and bash).  There is something called an environment associated with every running process which can contain variables that may affect the behavior of said process.  Generally, environment variables are set by the appropriate shell configuration files, or perhaps the configuration files of whatever graphical desktop environment you are using.  There are also configuration files for libraries, like .inputrc for readline and .gtkrc* for GTK, which will affect every application that uses the library.  No, there is no global hierarchy for configuration files.  Again, refer to the documentation for the specific program in question, for example, the bash manual for bash.  A general convention you can usually rely on is that user settings in $HOME override system-wide configuration in /etc.  This is typically accomplished by reading the user file after the system one, so that later settings overwrite earlier ones.  However, this is not a guarantee, and for definitive answers you should refer to the documentation for the specific program you are using.There is no class, at least none general enough to encompass all the files you've listed in your question, so the question of a reference for such a class is moot.  Again, refer to the documentation of the specific program you are using.