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By default, Muse expects all project files to have the file extension .muse. Files without this extension will not be associated with Muse mode and will not be considered part of any project, even if they are within a project directory.
If you don't want to use .muse, you can customize the extension
by setting the value of muse-file-extension.
If you don't want to use any extension at all, and want Muse to autodetect project files based on their location, then add the following to your Muse settings file.
(setq muse-file-extension nil
muse-mode-auto-p t)
Note that if you chose to have muse-file-extension set to
nil, you may have trouble if your .emacs file or other
init scripts attempt to visit a Muse file. (A very common example of
this is if you use Planner with Muse and run (plan) from your
.emacs.) If you wish to visit Muse files from your
.emacs, be sure to also add the following additional code before
any such visits happen:
(add-hook 'find-file-hooks 'muse-mode-maybe)