Zsh/Bash startup files loading order (.bashrc, .zshrc etc.)

The issue is that Bash sources from a different file based on what kind of shell it thinks it is in. For an “interactive non-login shell”, it reads .bashrc, but for an “interactive login shell” it reads from the first of .bash_profile, .bash_login and .profile (only). There is no sane reason why this should be so; it’s just historical. Follows in more detail.

For Bash, they work as follows. Read down the appropriate column. Executes A, then B, then C, etc. The B1, B2, B3 means it executes only the first of those files found.

+----------------+-----------+-----------+------+
|                |Interactive|Interactive|Script|
|                |login      |non-login  |      |
+----------------+-----------+-----------+------+
|/etc/profile    |   A       |           |      |
+----------------+-----------+-----------+------+
|/etc/bash.bashrc|           |    A      |      |
+----------------+-----------+-----------+------+
|~/.bashrc       |           |    B      |      |
+----------------+-----------+-----------+------+
|~/.bash_profile |   B1      |           |      |
+----------------+-----------+-----------+------+
|~/.bash_login   |   B2      |           |      |
+----------------+-----------+-----------+------+
|~/.profile      |   B3      |           |      |
+----------------+-----------+-----------+------+
|BASH_ENV        |           |           |  A   |
+----------------+-----------+-----------+------+
|                |           |           |      |
+----------------+-----------+-----------+------+
|                |           |           |      |
+----------------+-----------+-----------+------+
|~/.bash_logout  |    C      |           |      |
+----------------+-----------+-----------+------+

Typically, most users will encounter a login shell only if either:
* they logged in from a tty, not through a GUI
* they logged in remotely, such as through ssh.
If the shell was started any other way, such as through GNOME’s gnome-terminal or KDE’s konsole, then it is typically not a login shell — the login shell was what started GNOME or KDE behind your back when you logged in; things started anew are not login shells. New terminals or new screen windows you open are not login shells either. (Starting a new window in OS X’s Terminal.app seems to count as a login shell, though.)

So typically (or sooner or later), what you will encounter are non-login shells. So this case is what you should write your config files for. This means putting most of your stuff in ~/.bashrc, having exactly one of~/.bash_profile, ~/.bash_login, and ~/.profile, and sourcing ~/.bashrc from it. If you have nothing that you specifically want to happen only for login shells, you can even symlink one of the three to~/.bashrc. In fact, even if you do, it is probably a good idea to have only file, as follows:

# Bash customisation file

#General configuration starts: stuff that you always want executed

#General configuration ends

if [[ -n $PS1 ]]; then
    : # These are executed only for interactive shells
    echo "interactive"
else
    : # Only for NON-interactive shells
fi

if shopt -q login_shell ; then
    : # These are executed only when it is a login shell
    echo "login"
else
    : # Only when it is NOT a login shell
    echo "nonlogin"
fi

Almost everything should go in the “general configuration” section. There might be some commands (those which produce output, etc.) that you only want executed when the shell is interactive, and not in scripts, which you can put in the first “conditional section”. I don’t see any reason to use the rest. You can drop the “echo” lines, but keep the “:”s — they are commands which do nothing, and are needed if that section is empty.

You then need to have only file, and you can call this ~/.bashrc and do cd && ln -s .bashrc .bash_profile

For zsh: [Note that zsh seems to read ~/.profile as well, if ~/.zshrc is not present.]

+----------------+-----------+-----------+------+
|                |Interactive|Interactive|Script|
|                |login      |non-login  |      |
+----------------+-----------+-----------+------+
|/etc/zshenv     |    A      |    A      |  A   |
+----------------+-----------+-----------+------+
|~/.zshenv       |    B      |    B      |  B   |
+----------------+-----------+-----------+------+
|/etc/zprofile   |    C      |           |      |
+----------------+-----------+-----------+------+
|~/.zprofile     |    D      |           |      |
+----------------+-----------+-----------+------+
|/etc/zshrc      |    E      |    C      |      |
+----------------+-----------+-----------+------+
|~/.zshrc        |    F      |    D      |      |
+----------------+-----------+-----------+------+
|/etc/zlogin     |    G      |           |      |
+----------------+-----------+-----------+------+
|~/.zlogin       |    H      |           |      |
+----------------+-----------+-----------+------+
|                |           |           |      |
+----------------+-----------+-----------+------+
|                |           |           |      |
+----------------+-----------+-----------+------+
|~/.zlogout      |    I      |           |      |
+----------------+-----------+-----------+------+
|/etc/zlogout    |    J      |           |      |
+----------------+-----------+-----------+------+

Moral:
For bash, put stuff in ~/.bashrc, and make ~/.bash_profile source it.
For zsh, put stuff in ~/.zshrc, which is always executed.

[Note: This is assuming you care only about interactive shells (shells you can type at). If further you ever use non-interactive shells (like “ssh [host] [command]” which executes [command] on [host] and logs out immediately) and there is something you absolutely absolutely want executed first even for these cases (think carefully: they can interfere in strange ways and you may be able to do without them), then you can put such stuff in ~/.zshenv. For bash, put them in a file and set the value of BASH_ENV to the filename.]