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When I type $PATH, among the list of values I see some are from /etc/paths and /etc/paths.d, but there are also links to python frameworks. Where does it read these from?

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When you log on to your computer, the loginwindow.app sets up a basic environment which includes $HOME, $SHELL, $TMPDIR, $LOGNAME, $USER, and $PATH. The environment may also be altered by launch daemons or agent. Or by extending the PATH variable within launchd. Typically, the PATH variable is set to the hard coded PATH variable in the kernel.

sysctl user.cs_path
user.cs_path: /usr/bin:/bin:/usr/sbin:/sbin

When you start the terminal emulator, by default, it will call login - login -pf <yourname> which will setup only those environment variables that have not already set (see man login).

Your shell- $SHELL then reads the appropriate file in /etc that calls path_helper. path_helper takes the PATH variable that is already set, reads /etc/paths, removes duplicates in the current PATH and orders the PATH variable as set in /etc/paths, then reads the files within /etc/paths.d adds those to the PATH variable, and then adds any paths that were in the original PATH which haven't already been added..

Finally, your $SHELL reads the appropriate rc file for a login shell in your home directory.

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A program called path_helper is run from various /etc/* shell rc files by default.

$ grep path_helper /etc/* 2>/dev/null
/etc/csh.login:#if ( -x /usr/libexec/path_helper ) then
/etc/csh.login:#    eval `/usr/libexec/path_helper -c`
/etc/profile:#if [ -x /usr/libexec/path_helper ]; then
/etc/profile:#  eval `/usr/libexec/path_helper -s`
/etc/zprofile:#if [ -x /usr/libexec/path_helper ]; then
/etc/zprofile:# eval `/usr/libexec/path_helper -s`
$ 

This is obviously not the default; I've disabled path_helper and manage PATH in my own rc files.

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