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

2 files changed, 16 insertions, 13 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,
   );
 
diff --git a/cli/tools/registry/pm.rs b/cli/tools/registry/pm.rs
index 4573f196d..233e68240 100644
--- a/cli/tools/registry/pm.rs
+++ b/cli/tools/registry/pm.rs
@@ -119,9 +119,9 @@ impl DenoOrPackageJson {
   /// creates a `deno.json` file - in this case
   /// we also return a new `CliFactory` that knows about
   /// the new config
-  fn from_flags(flags: Flags) -> Result<(Self, CliFactory), AnyError> {
-    let factory = CliFactory::from_flags(flags.clone())?;
-    let options = factory.cli_options();
+  fn from_flags(flags: Arc<Flags>) -> Result<(Self, CliFactory), AnyError> {
+    let factory = CliFactory::from_flags(flags.clone());
+    let options = factory.cli_options()?;
     let start_dir = &options.start_dir;
 
     match (start_dir.maybe_deno_json(), start_dir.maybe_pkg_json()) {
@@ -142,8 +142,8 @@ impl DenoOrPackageJson {
           .context("Failed to create deno.json file")?;
         drop(factory); // drop to prevent use
         log::info!("Created deno.json configuration file.");
-        let factory = CliFactory::from_flags(flags.clone())?;
-        let options = factory.cli_options().clone();
+        let factory = CliFactory::from_flags(flags.clone());
+        let options = factory.cli_options()?.clone();
         let start_dir = &options.start_dir;
         Ok((
           DenoOrPackageJson::Deno(
@@ -175,7 +175,10 @@ fn package_json_dependency_entry(
   }
 }
 
-pub async fn add(flags: Flags, add_flags: AddFlags) -> Result<(), AnyError> {
+pub async fn add(
+  flags: Arc<Flags>,
+  add_flags: AddFlags,
+) -> Result<(), AnyError> {
   let (config_file, cli_factory) =
     DenoOrPackageJson::from_flags(flags.clone())?;
 
@@ -307,9 +310,9 @@ pub async fn add(flags: Flags, add_flags: AddFlags) -> Result<(), AnyError> {
   // clear the previously cached package.json from memory before reloading it
   deno_node::PackageJsonThreadLocalCache::clear();
   // make a new CliFactory to pick up the updated config file
-  let cli_factory = CliFactory::from_flags(flags)?;
+  let cli_factory = CliFactory::from_flags(flags);
   // cache deps
-  if cli_factory.cli_options().enable_future_features() {
+  if cli_factory.cli_options()?.enable_future_features() {
     crate::module_loader::load_top_level_deps(&cli_factory).await?;
   }