Fixes#1366
When we use `loadTheme`, we "replay" the configuration so that the theme
is the base configuration and everything else can override everything
the theme sets. During this process, we were not properly re-expanding
all the relative paths.
This fix works by changing our input tracking from solely tracking args
to tracking operations such as expansion as well. When we "replay" the
configuration we also replay operations such as path expansion with the
correct base path.
This also removes the `_inputs` special mechanism `cli/args.zig` had
because we can already do that ourselves using `parseManuallyHook`.