My file configuration is the following
and in my home directory I have symlinks
~/maildir/ --> /STORAGE/maildir
~/.mu/ --> /STORAGE/mu-index
I do this in order to save space in the home directory which is under quota.
When I index with the command 'mu index --maildir ~/maildir' the messages appear
(in mu4e-view) to be located in /STORAGE/maildir/.
Instead if index from emacs/mu4e the messages appear to be located in ~/maildir/.
My mu4e-maildir is set to (concat (getenv "HOME) "/maildir")
If I do indexing/update from both, then I get double messages everywhere, since mu4e believes that the two file system entry points to a message file are actually two distinct messages.
A workaround would be to hardcode in mu4e-maildir the actual path "/STORAGE/maildir", but I share the configuration on other computers where the maildir is actually in "~/maildir".
Does it depend on the shell executing 'mu index --maildir ~/maildir'? This happens both when the indexing command is launched by offlineimap, and when I launch it from the command line.