diff --git a/README.md b/README.md
index 6dada38..c6dfa5c 100644
--- a/README.md
+++ b/README.md
@@ -50,6 +50,7 @@ numd run --help
 # =>   -h, --help: Display the help message for this command
 # =>   --echo: output resulting markdown to stdout instead of saving to file
 # =>   --eval <string>: Nushell code to prepend to the script (use `open -r config.nu` for file-based config)
+# =>   --ignore-git-check: skip the check for uncommitted changes before overwriting
 # =>   --no-fail-on-error: skip errors (markdown is never saved on error)
 # =>   --no-stats: do not output stats of changes (is activated via --echo by default)
 # =>   --print-block-results: print blocks one by one as they are executed, useful for long running scripts
@@ -96,7 +97,7 @@ By default, `numd` provides basic stats on changes made (when not using `--echo`
 ```nushell
 # Running without --echo saves the file and returns stats
 let path = [z_examples 1_simple_markdown simple_markdown_with_no_output.md] | path join
-numd run $path
+numd run $path --ignore-git-check
 # => ╭──────────────────┬───────────────────────────────────╮
 # => │ filename         │ simple_markdown_with_no_output.md │
 # => │ nushell_blocks   │ 3                                 │
@@ -138,6 +139,8 @@ numd run $path --echo --no-stats --eval "
 ```nu
 numd clear-outputs --help
 # => Remove numd execution outputs from the file
+# => Note: No git check here - clearing outputs is a reversible operation (just re-run numd)
+# => and users typically clear outputs intentionally before committing clean source
 # =>
 # => Usage:
 # =>   > clear-outputs {flags} <file>
diff --git a/numd/commands.nu b/numd/commands.nu
index e4a1707..3082327 100644
--- a/numd/commands.nu
+++ b/numd/commands.nu
@@ -8,6 +8,7 @@ export def run [
     file: path # path to a `.md` file containing Nushell code to be executed
     --echo # output resulting markdown to stdout instead of saving to file
     --eval: string # Nushell code to prepend to the script (use `open -r config.nu` for file-based config)
+    --ignore-git-check # skip the check for uncommitted changes before overwriting
     --no-fail-on-error # skip errors (markdown is never saved on error)
     --no-stats # do not output stats of changes (is activated via --echo by default)
     --print-block-results # print blocks one by one as they are executed, useful for long running scripts
@@ -38,7 +39,7 @@ export def run [
     if $echo {
         $updated_md
     } else {
-        check-git-clean $file
+        if not $ignore_git_check { check-git-clean $file }
         $updated_md | ansi strip | save -f $file
 
         if not $no_stats {
@@ -48,6 +49,8 @@ export def run [
 }
 
 # Remove numd execution outputs from the file
+# Note: No git check here - clearing outputs is a reversible operation (just re-run numd)
+# and users typically clear outputs intentionally before committing clean source
 export def clear-outputs [
     file: path # path to a `.md` file containing numd output to be cleared
     --echo # output resulting markdown to stdout instead of writing to file
@@ -61,9 +64,7 @@ export def clear-outputs [
         to-markdown
     }
     | if $echo { } else {
-        let result = $in
-        check-git-clean $file
-        $result | save -f $file
+        $in | save -f $file
     }
 }
 
@@ -661,7 +662,7 @@ export def build-modified-path [
 }
 
 # Check if file is safely tracked in git before overwriting.
-# Warns if file has uncommitted changes or is not tracked by git.
+# Errors if file has uncommitted changes. Use --ignore-git-check to skip.
 export def check-git-clean [
     file_path: path # path to the file to check
 ]: nothing -> nothing {
@@ -671,18 +672,17 @@ export def check-git-clean [
     let in_git_repo = (do { git rev-parse --git-dir } | complete).exit_code == 0
     if not $in_git_repo { return }
 
-    # Check if file is tracked by git
+    # Check if file is tracked by git (untracked files are ok to overwrite)
     let is_tracked = (do { git ls-files --error-unmatch $file } | complete).exit_code == 0
-    if not $is_tracked {
-        print -e $"(ansi yellow)Warning: ($file_path) is not tracked by git(ansi reset)"
-        return
-    }
+    if not $is_tracked { return }
 
     # Check if file has uncommitted changes
     let has_changes = (git diff --name-only $file | str trim) != ''
     let is_staged = (git diff --staged --name-only $file | str trim) != ''
     if $has_changes or $is_staged {
-        print -e $"(ansi yellow)Warning: ($file_path) has uncommitted changes(ansi reset)"
+        error make --unspanned {
+            msg: $"($file_path) has uncommitted changes. Commit or stash changes first, or use --ignore-git-check to override."
+        }
     }
 }
 
diff --git a/toolkit.nu b/toolkit.nu
index 7362159..0556146 100644
--- a/toolkit.nu
+++ b/toolkit.nu
@@ -66,7 +66,7 @@ export def 'main test-integration' [
         # Run files with config set
         (
             numd run $file --save-intermed-script $'($file)_intermed.nu'
-            --eval (open -r numd_config_example1.nu)
+            --eval (open -r numd_config_example1.nu) --ignore-git-check
         )
     }
     # Run file with customized width of table
@@ -89,7 +89,7 @@ export def 'main test-integration' [
     })
     # Run readme
     | append (
-        numd run README.md --eval (open -r numd_config_example1.nu)
+        numd run README.md --eval (open -r numd_config_example1.nu) --ignore-git-check
     )
     | if $json { to json --raw } else { }
 }