4 files changed, 7 insertions, 4 deletions
diff --git a/cli/tools/coverage/mod.rs b/cli/tools/coverage/mod.rs
index ec77c1bb8..30d35878b 100644
--- a/cli/tools/coverage/mod.rs
+++ b/cli/tools/coverage/mod.rs
@@ -378,6 +378,7 @@ fn collect_coverages(
 ) -> Result<Vec<cdp::ScriptCoverage>, AnyError> {
   let mut coverages: Vec<cdp::ScriptCoverage> = Vec::new();
   let file_patterns = FilePatterns {
+    base: initial_cwd.to_path_buf(),
     include: Some({
       if files.include.is_empty() {
         PathOrPatternSet::new(vec![PathOrPattern::Path(
diff --git a/cli/tools/doc.rs b/cli/tools/doc.rs
index 7a51f6356..4321b3ce7 100644
--- a/cli/tools/doc.rs
+++ b/cli/tools/doc.rs
@@ -93,6 +93,7 @@ pub async fn doc(flags: Flags, doc_flags: DocFlags) -> Result<(), AnyError> {
 
       let module_specifiers = collect_specifiers(
         FilePatterns {
+          base: cli_options.initial_cwd().to_path_buf(),
           include: Some(PathOrPatternSet::from_relative_path_or_patterns(
             cli_options.initial_cwd(),
             source_files,
diff --git a/cli/tools/registry/mod.rs b/cli/tools/registry/mod.rs
index 20a1d70ae..d9d0663c6 100644
--- a/cli/tools/registry/mod.rs
+++ b/cli/tools/registry/mod.rs
@@ -128,7 +128,7 @@ async fn prepare_publish(
   };
   let exclude_patterns = deno_json
     .to_files_config()
-    .map(|files| files.unwrap_or_default().exclude)?;
+    .map(|files| files.map(|f| f.exclude).unwrap_or_default())?;
 
   let tarball = deno_core::unsync::spawn_blocking(move || {
     let unfurler = ImportMapUnfurler::new(&import_map);
diff --git a/cli/tools/vendor/mod.rs b/cli/tools/vendor/mod.rs
index 16897f1a5..e2c04305a 100644
--- a/cli/tools/vendor/mod.rs
+++ b/cli/tools/vendor/mod.rs
@@ -227,14 +227,15 @@ fn maybe_update_config_file(
     return ModifiedResult::default();
   }
 
-  let fmt_config = config_file
+  let fmt_config_options = config_file
     .to_fmt_config()
     .ok()
-    .unwrap_or_default()
+    .flatten()
+    .map(|config| config.options)
     .unwrap_or_default();
   let result = update_config_file(
     config_file,
-    &fmt_config.options,
+    &fmt_config_options,
     if try_add_import_map {
       Some(
         ModuleSpecifier::from_file_path(output_dir.join("import_map.json"))