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, 17 insertions, 15 deletions

diff --git a/cli/tools/run/mod.rs b/cli/tools/run/mod.rs
index f70cfd066..baa8e72db 100644
--- a/cli/tools/run/mod.rs
+++ b/cli/tools/run/mod.rs
@@ -1,6 +1,7 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
 use std::io::Read;
+use std::sync::Arc;
 
 use deno_core::error::AnyError;
 use deno_runtime::deno_permissions::Permissions;
@@ -11,7 +12,6 @@ use crate::args::EvalFlags;
 use crate::args::Flags;
 use crate::args::WatchFlagsWithPaths;
 use crate::factory::CliFactory;
-use crate::factory::CliFactoryBuilder;
 use crate::file_fetcher::File;
 use crate::util;
 use crate::util::file_watcher::WatcherRestartMode;
@@ -20,7 +20,7 @@ pub mod hmr;
 
 pub async fn run_script(
   mode: WorkerExecutionMode,
-  flags: Flags,
+  flags: Arc<Flags>,
   watch: Option<WatchFlagsWithPaths>,
 ) -> Result<i32, AnyError> {
   if !flags.has_permission() && flags.has_permission_in_argv() {
@@ -40,10 +40,10 @@ To grant permissions, set them before the script argument. For example:
 
   // TODO(bartlomieju): actually I think it will also fail if there's an import
   // map specified and bare specifier is used on the command line
-  let factory = CliFactory::from_flags(flags)?;
+  let factory = CliFactory::from_flags(flags);
+  let cli_options = factory.cli_options()?;
   let deno_dir = factory.deno_dir()?;
   let http_client = factory.http_client_provider();
-  let cli_options = factory.cli_options();
 
   if cli_options.unstable_sloppy_imports() {
     log::warn!(
@@ -76,9 +76,9 @@ To grant permissions, set them before the script argument. For example:
   Ok(exit_code)
 }
 
-pub async fn run_from_stdin(flags: Flags) -> Result<i32, AnyError> {
-  let factory = CliFactory::from_flags(flags)?;
-  let cli_options = factory.cli_options();
+pub async fn run_from_stdin(flags: Arc<Flags>) -> Result<i32, AnyError> {
+  let factory = CliFactory::from_flags(flags);
+  let cli_options = factory.cli_options()?;
   let main_module = cli_options.resolve_main_module()?;
 
   maybe_npm_install(&factory).await?;
@@ -109,7 +109,7 @@ pub async fn run_from_stdin(flags: Flags) -> Result<i32, AnyError> {
 // code properly.
 async fn run_with_watch(
   mode: WorkerExecutionMode,
-  flags: Flags,
+  flags: Arc<Flags>,
   watch_flags: WatchFlagsWithPaths,
 ) -> Result<i32, AnyError> {
   util::file_watcher::watch_recv(
@@ -122,9 +122,11 @@ async fn run_with_watch(
     WatcherRestartMode::Automatic,
     move |flags, watcher_communicator, _changed_paths| {
       Ok(async move {
-        let factory = CliFactoryBuilder::new()
-          .build_from_flags_for_watcher(flags, watcher_communicator.clone())?;
-        let cli_options = factory.cli_options();
+        let factory = CliFactory::from_flags_for_watcher(
+          flags,
+          watcher_communicator.clone(),
+        );
+        let cli_options = factory.cli_options()?;
         let main_module = cli_options.resolve_main_module()?;
 
         maybe_npm_install(&factory).await?;
@@ -156,11 +158,11 @@ async fn run_with_watch(
 }
 
 pub async fn eval_command(
-  flags: Flags,
+  flags: Arc<Flags>,
   eval_flags: EvalFlags,
 ) -> Result<i32, AnyError> {
-  let factory = CliFactory::from_flags(flags)?;
-  let cli_options = factory.cli_options();
+  let factory = CliFactory::from_flags(flags);
+  let cli_options = factory.cli_options()?;
   let file_fetcher = factory.file_fetcher()?;
   let main_module = cli_options.resolve_main_module()?;
 
@@ -195,7 +197,7 @@ pub async fn eval_command(
 async fn maybe_npm_install(factory: &CliFactory) -> Result<(), AnyError> {
   // ensure an "npm install" is done if the user has explicitly
   // opted into using a managed node_modules directory
-  if factory.cli_options().node_modules_dir_enablement() == Some(true) {
+  if factory.cli_options()?.node_modules_dir_enablement() == Some(true) {
     if let Some(npm_resolver) = factory.npm_resolver().await?.as_managed() {
       npm_resolver.ensure_top_level_package_json_install().await?;
     }