feat: sparse checkout deny-all-by-default (modified cone pattern) with opt-out support (#48)

Co-authored-by: bashandbone <89049923+bashandbone@users.noreply.github.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

Author: Copilot

sample_config/submod.toml

@@ -49,14 +49,27 @@ ignore = "dirty" # Override default ignore setting for all submodules
 #
 # ## `sparse_paths`
 # A list of relative paths or glob patterns to include in the sparse checkout. If omitted, includes all files.
-# If set, git prepends:
-# ```git
-# /*
-# !/*/
+# **Deny-all by default:** `submod` automatically prepends `!/*` as the first pattern,
+# so _only_ the paths you list are checked out. You declare what you want; everything
+# else is excluded. No manual negation rules are needed for the common case.
+# Example — check out only `src/`, `include/`, and markdown files at any depth:
+# ```toml
+# sparse_paths = ["src/", "include/", "*.md"]
+# ```
+# This writes the following patterns to git's sparse-checkout file:
 # ```
-# This includes only files in the root directory, excluding subdirectories.
-# To exclude root files, prefix with `!` (e.g., `!/README.md`).
-# To include subdirectories, add paths like `/src/`.
+# !/*        ← deny all by default (added automatically)
+# src/       ← include src/
+# include/   ← include include/
+# *.md       ← include markdown files at any depth
+# ```
+# To match markdown files only at the repository root use `/*.md` instead.
+# Any `!/*` entries you add yourself are de-duplicated automatically.
+#
+# ## `use_git_default_sparse_checkout`
+# Set to `true` to opt out of submod's deny-all-by-default model for this submodule
+# and use git's standard sparse-checkout semantics instead (no automatic `!/*` prefix).
+# Can also be set globally under `[defaults]`.
 #
 # ## `shallow`
 #
@@ -73,7 +86,7 @@ url = "https://github.com/example/utils.git"
 sparse_paths = [
     "src/",      # All files in src directory
     "include/",  # All files in include directory
-    "*.md"       # All markdown files in submodule root
+    "*.md"       # All markdown files at any depth
 ]
 ignore = "all"   # Override default ignore setting
 

src/commands.rs

@@ -120,6 +120,15 @@ pub enum Commands {
         )]
         sparse_paths: Option<Vec<String>>,
 
+        #[arg(
+            long = "use-git-default-sparse-checkout",
+            num_args = 0..=1,
+            value_parser = clap::value_parser!(bool),
+            default_missing_value = "true",
+            help = "Opt out of submod's deny-all-by-default sparse-checkout model and use git's built-in behaviour instead. When set, the `!/*` prefix is NOT prepended automatically."
+        )]
+        use_git_default_sparse_checkout: Option<bool>,
+
         #[arg(
             short = 'f',
             long = "fetch",
@@ -166,6 +175,15 @@ pub enum Commands {
         #[arg(requires("sparse_paths"), short = 'a', long = "append", value_parser = clap::value_parser!(bool), default_value = "false", default_missing_value = "true", help = "If given, appends the new sparse paths to the existing ones.")]
         append: bool,
 
+        #[arg(
+            long = "use-git-default-sparse-checkout",
+            num_args = 0..=1,
+            value_parser = clap::value_parser!(bool),
+            default_missing_value = "true",
+            help = "Opt out of submod's deny-all-by-default sparse-checkout model and use git's built-in behaviour instead."
+        )]
+        use_git_default_sparse_checkout: Option<bool>,
+
         #[arg(
             short = 'i',
             long = "ignore",
@@ -224,6 +242,15 @@ pub enum Commands {
             help = "Sets the default update behavior for all submodules in this repository. This will override any individual submodule settings."
         )]
         update: Option<Update>,
+
+        #[arg(
+            long = "use-git-default-sparse-checkout",
+            num_args = 0..=1,
+            value_parser = clap::value_parser!(bool),
+            default_missing_value = "true",
+            help = "Set the global default for sparse-checkout mode. When true, all submodules use git's built-in behaviour instead of submod's deny-all-by-default model (unless overridden per-submodule)."
+        )]
+        use_git_default_sparse_checkout: Option<bool>,
     },
 
     #[command(

src/config.rs

@@ -166,6 +166,11 @@ pub struct SubmoduleDefaults {
     pub fetch_recurse: Option<SerializableFetchRecurse>,
     /// [`Update`][SerializableUpdate] setting for submodules
     pub update: Option<SerializableUpdate>,
+    /// When `true`, use git's built-in sparse-checkout behaviour (no `!/*` prefix is
+    /// prepended). Defaults to `false`, which uses submod's deny-all-by-default model.
+    /// Individual submodules can override this per-entry.
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub use_git_default_sparse_checkout: Option<bool>,
 }
 
 impl Iterator for SubmoduleDefaults {
@@ -204,6 +209,7 @@ impl SubmoduleDefaults {
                     .fetch_recurse
                     .or_else(|| Some(SerializableFetchRecurse::default())),
                 update: update.or_else(|| Some(SerializableUpdate::default())),
+                use_git_default_sparse_checkout: mut_self.use_git_default_sparse_checkout,
             }
         }
     }
@@ -248,6 +254,7 @@ impl SubmoduleAddOptions {
             active: Some(!self.no_init), // we're adding so unless we have a 'no_init" flag, we can assume active
             no_init: Some(self.no_init),
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         }
     }
 
@@ -460,6 +467,10 @@ pub struct SubmoduleEntry {
     /// Sparse checkout paths for this submodule (optional)
     #[serde(skip_serializing_if = "Option::is_none")]
     pub sparse_paths: Option<Vec<String>>,
+    /// When `true`, use git's built-in sparse-checkout behaviour instead of submod's
+    /// deny-all-by-default model.  Overrides the global `[defaults]` setting.
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub use_git_default_sparse_checkout: Option<bool>,
 }
 
 #[allow(dead_code)]
@@ -487,6 +498,7 @@ impl SubmoduleEntry {
             shallow: shallow,
             no_init: no_init,
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         }
     }
 
@@ -666,6 +678,7 @@ impl From<OtherSubmoduleSettings> for SubmoduleEntry {
             update: default_git_options.update,
             no_init: Some(other.no_init),
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         }
     }
 }
@@ -1152,11 +1165,13 @@ mod tests {
             ignore: Some(SerializableIgnore::All),
             fetch_recurse: Some(SerializableFetchRecurse::Always),
             update: Some(SerializableUpdate::Rebase),
+            use_git_default_sparse_checkout: None,
         };
         let other = SubmoduleDefaults {
             ignore: Some(SerializableIgnore::Dirty),
             fetch_recurse: None,
             update: Some(SerializableUpdate::Merge),
+            use_git_default_sparse_checkout: None,
         };
         let merged = base.merge_from(other);
         // other.ignore overrides
@@ -1173,6 +1188,7 @@ mod tests {
             ignore: Some(SerializableIgnore::All),
             fetch_recurse: Some(SerializableFetchRecurse::Never),
             update: Some(SerializableUpdate::Checkout),
+            use_git_default_sparse_checkout: None,
         };
         let other = SubmoduleDefaults::default();
         let merged = base.merge_from(other);
@@ -1189,6 +1205,7 @@ mod tests {
             ignore: Some(SerializableIgnore::Dirty),
             fetch_recurse: Some(SerializableFetchRecurse::Always),
             update: Some(SerializableUpdate::Merge),
+            use_git_default_sparse_checkout: None,
         };
         let merged = base.merge_from(other);
         assert_eq!(merged.ignore, Some(SerializableIgnore::Dirty));
@@ -1572,6 +1589,7 @@ mod tests {
             shallow: None,
             no_init: None,
             sparse_paths: Some(vec!["src/".to_string()]),
+            use_git_default_sparse_checkout: None,
         };
         entries.update_entry("repo".to_string(), entry);
 
@@ -1597,6 +1615,7 @@ mod tests {
             shallow: None,
             no_init: None,
             sparse_paths: Some(vec!["src/".to_string()]),
+            use_git_default_sparse_checkout: None,
         };
         entries.update_entry("repo".to_string(), entry_with_sparse);
         assert!(entries.sparse_checkouts().unwrap().contains_key("repo"));
@@ -1613,6 +1632,7 @@ mod tests {
             shallow: None,
             no_init: None,
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         };
         entries.update_entry("repo".to_string(), entry_no_sparse);
         assert!(!entries.sparse_checkouts().unwrap().contains_key("repo"));
@@ -1779,6 +1799,7 @@ mod tests {
             ignore: Some(SerializableIgnore::Dirty),
             fetch_recurse: Some(SerializableFetchRecurse::Always),
             update: Some(SerializableUpdate::Rebase),
+            use_git_default_sparse_checkout: None,
         };
         let entry = SubmoduleEntry::new(
             Some("url".to_string()),
@@ -1808,6 +1829,7 @@ mod tests {
             ignore: Some(SerializableIgnore::Dirty),
             fetch_recurse: Some(SerializableFetchRecurse::Always),
             update: Some(SerializableUpdate::Rebase),
+            use_git_default_sparse_checkout: None,
         };
         let entry = SubmoduleEntry::new(
             Some("url".to_string()),
@@ -1900,6 +1922,7 @@ mod tests {
             shallow: None,
             no_init: None,
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         };
         let opts = SubmoduleAddOptions::from_submodule_entries_tuple(("mymod".to_string(), entry));
         // url fallback: path
@@ -1920,6 +1943,7 @@ mod tests {
             shallow: None,
             no_init: None,
             sparse_paths: None,
+            use_git_default_sparse_checkout: None,
         };
         let opts = SubmoduleAddOptions::from_submodule_entries_tuple(("mymod".to_string(), entry));
         // Falls back to name for both url and path
@@ -1972,6 +1996,7 @@ mod tests {
             shallow: Some(false),
             no_init: None,
             sparse_paths: Some(vec!["src/".to_string()]),
+            use_git_default_sparse_checkout: None,
         };
         entries = entries.add_submodule("mymod".to_string(), entry);