fix handling of static/volume dir

The processing and setting of the static and volume directories was
scattered across the code base (including c/common) leading to subtle
errors that surfaced in #19938.

There were multiple issues that I try to summarize below:

 - c/common loaded the graphroot from c/storage to set the defaults for
   static and volume dir.  That ignored Podman's --root flag and
   surfaced in #19938 and other bugs.  c/common does not set the
   defaults anymore which gives Podman the ability to detect when the
   user/admin configured a custom directory (not empty value).

 - When parsing the CLI, Podman (ab)uses containers.conf structures to
   set the defaults but also to override them in case the user specified
   a flag.  The --root flag overrode the static dir which is wrong and
   broke a couple of use cases.  Now there is a dedicated field for in
   the "PodmanConfig" which also includes a containers.conf struct.

 - The defaults for static and volume dir and now being set correctly
   and adhere to --root.

 - The CONTAINERS_CONF_OVERRIDE env variable has not been passed to the
   cleanup process.  I believe that _all_ env variables should be passed
   to conmon to avoid such subtle bugs.

Overall I find that the code and logic is scattered and hard to
understand and follow.  I refrained from larger refactorings as I really
just want to get #19938 fixed and then go back to other priorities.

https://github.com/containers/common/pull/1659 broke three pkg/machine
tests.  Those have been commented out until getting fixed.

Fixes: #19938
Signed-off-by: Valentin Rothberg <vrothberg@redhat.com>

libpod/sqlite_state.go

@@ -54,6 +54,8 @@ func NewSqliteState(runtime *Runtime) (_ State, defErr error) {
 	basePath := runtime.storageConfig.GraphRoot
 	if runtime.storageConfig.TransientStore {
 		basePath = runtime.storageConfig.RunRoot
+	} else if !runtime.storageSet.StaticDirSet {
+		basePath = runtime.config.Engine.StaticDir
 	}
 
 	// c/storage is set up *after* the DB - so even though we use the c/s