fix(upgrade): do not error if config in cwd invalid (#24689)

```
> deno upgrade
error: Unsupported lockfile version 'invalid'. Try upgrading Deno or recreating the lockfile.
V:\scratch
> V:\deno\target\debug\deno upgrade
Looking up latest version
Local deno version 1.45.3 is the most recent release
```

Closes #24517
Closes #20729

1 files changed, 5 insertions, 5 deletions

diff --git a/cli/tools/registry/mod.rs b/cli/tools/registry/mod.rs
index 1c4e1bea7..bf9ce8586 100644
--- a/cli/tools/registry/mod.rs
+++ b/cli/tools/registry/mod.rs
@@ -72,16 +72,16 @@ use self::paths::CollectedPublishPath;
 use self::tar::PublishableTarball;
 
 pub async fn publish(
-  flags: Flags,
+  flags: Arc<Flags>,
   publish_flags: PublishFlags,
 ) -> Result<(), AnyError> {
-  let cli_factory = CliFactory::from_flags(flags)?;
+  let cli_factory = CliFactory::from_flags(flags);
 
   let auth_method =
     get_auth_method(publish_flags.token, publish_flags.dry_run)?;
 
-  let directory_path = cli_factory.cli_options().initial_cwd();
-  let cli_options = cli_factory.cli_options();
+  let cli_options = cli_factory.cli_options()?;
+  let directory_path = cli_options.initial_cwd();
   let publish_configs = cli_options.start_dir.jsr_packages_for_publish();
   if publish_configs.is_empty() {
     match cli_options.start_dir.maybe_deno_json() {
@@ -121,7 +121,7 @@ pub async fn publish(
     cli_factory.module_graph_creator().await?.clone(),
     cli_factory.parsed_source_cache().clone(),
     cli_factory.type_checker().await?.clone(),
-    cli_factory.cli_options().clone(),
+    cli_options.clone(),
     specifier_unfurler,
   );