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configure*: Move AC_SUBST calls to more obvious places
These macros should always be called regardless of the intended value of each variable, as even if e.g.: no --enable-apparmor flag is given, the configure script still has to substitute `@HAVE_APPARMOR@` with blank in the relevant files. Something similar is already being done for HAVE_OVERLAYFS since commit fb9f2a5 ("disabled overlayfs, fixes pending; added video channels to README* files", 2021-02-06). Note that each AC_SUBST is not immediately converted into search/replace code when generating the configure script. It appears that the variables are handled only after parsing all of configure.ac (or until a specific command is found), as all arguments passed to every AC_SUBST call are defined at once on the `ac_subst_vars` list. The actual substitutions are also done all at once (while iterating through the list) and that happens much later in the script (see both occurrences of `ac_subs_vars` on the current script).
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