mu: Default to XDG Base Directory Specification

Instead of using ~/.mu, use the XDG Base Directory Specification, typically:
  ~/.cache/xapian
  ~/.cache/mu.log
  ~/.cache/parts
  ~/.config/bookmarks

Update dependencies, documentation.

lib/Makefile.am

@@ -64,7 +64,6 @@ libmu_la_SOURCES=				\
 	mu-bookmarks.h				\
 	mu-contacts.cc				\
 	mu-contacts.hh				\
-	mu-contacts.h				\
 	mu-container.c				\
 	mu-container.h				\
 	mu-date.c				\
@@ -98,7 +97,7 @@ libmu_la_SOURCES=				\
 	mu-msg.h				\
 	mu-query.cc				\
 	mu-query.h				\
-	mu-runtime.c				\
+	mu-runtime.cc				\
 	mu-runtime.h				\
 	mu-script.c				\
 	mu-script.h				\
@@ -125,7 +124,6 @@ libmu_la_LIBADD=				\
 libmu_la_LDFLAGS=				\
 	$(ASAN_LDFLAGS)
 
-
 EXTRA_DIST=					\
 	mu-msg-crypto.c				\
 	doxyfile.in