Reindex checks install for non-external packages (#4027)

Fixes #4026

#1167 updated Database.reindex to keep old installation records to
support external packages. However, when a user manually removes a
prefix and reindexes this kept the records so the packages were
still installed according to "spack find" etc. This adds a check
for non-external packages to ensure they are properly installed
according to the directory layout.

lib/spack/spack/database.py

@@ -473,6 +473,11 @@ def _read_suppress_error():
                         layout = spack.store.layout
                         if entry.spec.external:
                             layout = None
+                            install_check = True
+                        else:
+                            install_check = layout.check_installed(entry.spec)
+
+                        if install_check:
                             kwargs = {
                                 'spec': entry.spec,
                                 'directory_layout': layout,