bugfix: reindexing is not necessary for DB v0.9.3 to v5 upgrade (#13434)

reindexing takes a significant amount of time, and there's no reason to
do it from DB version 0.9.3 to version 5. The only difference is that v5
can contain "deprecated_for" fields.

- [x] Add a `_skip_reindex` list at the start of `database.py`

- [x] Skip the reindex for upgrades in this list. The new version will
  just be written to the file the first time we actually have to write
  the DB out (e.g., after an install), and reads will still work fine.

lib/spack/spack/database.py

@@ -51,9 +51,20 @@
 
 # DB version.  This is stuck in the DB file to track changes in format.
 # Increment by one when the database format changes.
-# versions before 5 were not integers
+# Versions before 5 were not integers.
 _db_version = Version('5')
 
+# For any version combinations here, skip reindex when upgrading.
+# Reindexing can take considerable time and is not always necessary.
+_skip_reindex = [
+    # reindexing takes a significant amount of time, and there's
+    # no reason to do it from DB version 0.9.3 to version 5. The
+    # only difference is that v5 can contain "deprecated_for"
+    # fields.  So, skip the reindex for this transition. The new
+    # version is saved to disk the first time the DB is written.
+    (Version('0.9.3'), Version('5')),
+]
+
 # Timeout for spack database locks in seconds
 _db_lock_timeout = 120
 
@@ -486,8 +497,19 @@ def check(cond, msg):
         if version > _db_version:
             raise InvalidDatabaseVersionError(_db_version, version)
         elif version < _db_version:
-            self.reindex(spack.store.layout)
-            installs = dict((k, v.to_dict()) for k, v in self._data.items())
+            if not any(
+                    old == version and new == _db_version
+                    for old, new in _skip_reindex
+            ):
+                tty.warn(
+                    "Spack database version changed from %s to %s. Upgrading."
+                    % (version, _db_version)
+                )
+
+                self.reindex(spack.store.layout)
+                installs = dict(
+                    (k, v.to_dict()) for k, v in self._data.items()
+                )
 
         def invalid_record(hash_key, error):
             msg = ("Invalid record in Spack database: "