diff --git a/src/context/local.rs b/src/context/local.rs
index 6e161a8..3ed5c56 100644
--- a/src/context/local.rs
+++ b/src/context/local.rs
@@ -173,6 +173,15 @@ fn copy_dir_recursive(src: &Path, dest: &Path) -> io::Result<()> {
         for entry in std::fs::read_dir(src)? {
             let entry = entry?;
             let path = entry.path();
+            // Never ship VCS metadata into the build tree: its presence
+            // flips autotools 'building from VCS' detection (see
+            // is_vcs_dir_name) and activates maintainer-only regeneration
+            // rules requiring undeclared tools (e.g. help2man).
+            if path.symlink_metadata().map(|m| m.is_dir()).unwrap_or(false)
+                && super::is_vcs_dir_name(&entry.file_name())
+            {
+                continue;
+            }
             let dest_path = dest.join(entry.file_name());
             copy_dir_recursive(&path, &dest_path)?;
         }
diff --git a/src/context/mod.rs b/src/context/mod.rs
index 862c217..e0bd280 100644
--- a/src/context/mod.rs
+++ b/src/context/mod.rs
@@ -20,6 +20,49 @@ pub fn current() -> Arc<Context> {
     manager::MANAGER.current()
 }
 
+/// Version-control metadata directories that must never leak into a
+/// prepared build tree.
+///
+/// Their presence flips autotools' "building from VCS" detection (e.g. GNU
+/// hello's `BUILD_FROM_GIT`, triggered by a `.git` directory next to
+/// `configure.ac`), which activates maintainer-only regeneration rules
+/// requiring tools that are deliberately not declared as build-dependencies
+/// (e.g. `help2man`). Source packages produced by dpkg-source never contain
+/// them, so package builds must not see them either.
+pub(crate) fn is_vcs_dir_name(name: &std::ffi::OsStr) -> bool {
+    matches!(
+        name.to_str(),
+        Some(".git") | Some(".hg") | Some(".svn") | Some(".bzr") | Some("CVS")
+    )
+}
+
+/// Recursively remove version-control metadata directories below `root`.
+///
+/// Used after an overlay mount, where the source tree is exposed verbatim
+/// and entries cannot be filtered during the copy.
+pub(crate) fn prune_vcs_dirs(root: &std::path::Path) -> std::io::Result<()> {
+    let mut pending = vec![root.to_path_buf()];
+    while let Some(dir) = pending.pop() {
+        for entry in std::fs::read_dir(&dir)? {
+            let entry = entry?;
+            let path = entry.path();
+            // symlink_metadata: never follow symlinks while pruning.
+            let Ok(meta) = std::fs::symlink_metadata(&path) else {
+                continue;
+            };
+            if meta.is_dir() {
+                if is_vcs_dir_name(&entry.file_name()) {
+                    log::debug!("Removing VCS metadata from build tree: {}", path.display());
+                    std::fs::remove_dir_all(&path)?;
+                } else {
+                    pending.push(path);
+                }
+            }
+        }
+    }
+    Ok(())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -178,4 +221,43 @@ mod tests {
             std::path::Path::new("/nonexistent/target")
         );
     }
+
+    /// Copying a source tree into a build context must strip version-control
+    /// metadata directories at any depth: their presence flips autotools
+    /// "building from git" detection and activates maintainer-only rules
+    /// needing undeclared tools (e.g. help2man for GNU hello's man page).
+    #[test]
+    fn test_ensure_available_strips_vcs_metadata() {
+        let temp_dir = tempfile::tempdir().unwrap();
+        let src_root = temp_dir.path().join("pkg");
+        fs::create_dir_all(src_root.join(".git/objects")).unwrap();
+        fs::write(src_root.join(".git/HEAD"), "ref: refs/heads/main").unwrap();
+        fs::create_dir_all(src_root.join("src/.svn")).unwrap();
+        fs::write(src_root.join("src/hello.c"), "int main() {}").unwrap();
+
+        let ctx = Context::new(ContextConfig::Local);
+        let dest = ctx.ensure_available(&src_root, "/tmp").unwrap();
+
+        assert!(dest.join("src/hello.c").exists());
+        assert!(!dest.join(".git").exists());
+        assert!(!dest.join("src/.svn").exists());
+    }
+
+    /// The overlay-mount path exposes the tree verbatim, so pruning happens
+    /// after the fact: nested VCS metadata must be removed recursively.
+    #[test]
+    fn test_prune_vcs_dirs_removes_nested_metadata() {
+        let temp_dir = tempfile::tempdir().unwrap();
+        let root = temp_dir.path().join("tree");
+        fs::create_dir_all(root.join("a/.git/objects")).unwrap();
+        fs::create_dir_all(root.join("b/c/CVS")).unwrap();
+        fs::write(root.join("a/.git/HEAD"), "ref").unwrap();
+        fs::write(root.join("b/keep.txt"), "x").unwrap();
+
+        prune_vcs_dirs(&root).unwrap();
+
+        assert!(!root.join("a/.git").exists());
+        assert!(!root.join("b/c/CVS").exists());
+        assert!(root.join("b/keep.txt").exists());
+    }
 }
diff --git a/src/context/ssh.rs b/src/context/ssh.rs
index b33d671..d5d5b35 100644
--- a/src/context/ssh.rs
+++ b/src/context/ssh.rs
@@ -315,6 +315,14 @@ impl SshDriver {
                 let entry = entry?;
                 let path = entry.path();
                 let name = entry.file_name();
+                // Skip VCS metadata (see is_vcs_dir_name): shipping it into
+                // the remote build tree would flip autotools 'building from
+                // VCS' detection and activate maintainer-only rules.
+                if path.symlink_metadata().map(|m| m.is_dir()).unwrap_or(false)
+                    && super::is_vcs_dir_name(&name)
+                {
+                    continue;
+                }
                 let dest_path = dest.join(name);
                 Self::upload_recursive(sftp, &path, &dest_path)?;
             }
diff --git a/src/context/unshare.rs b/src/context/unshare.rs
index 31937cc..6847dae 100644
--- a/src/context/unshare.rs
+++ b/src/context/unshare.rs
@@ -55,6 +55,14 @@ fn copy_dir_recursive(src: &Path, dest: &Path) -> io::Result<()> {
             }
         };
 
+        // Never ship VCS metadata into the build tree: its presence flips
+        // autotools 'building from VCS' detection (see is_vcs_dir_name) and
+        // activates maintainer-only regeneration rules requiring tools that
+        // are not declared build-dependencies (e.g. help2man).
+        if metadata.is_dir() && super::is_vcs_dir_name(&entry.file_name()) {
+            continue;
+        }
+
         if metadata.file_type().is_symlink() {
             let target = std::fs::read_link(&src_path).map_err(|e| {
                 io::Error::new(
@@ -428,6 +436,20 @@ impl UnshareDriver {
             .lock()
             .unwrap()
             .push(dest_path.to_path_buf());
+
+        // The overlay exposes the source tree verbatim: strip VCS metadata
+        // (e.g. '.git') whose presence would flip autotools 'building from
+        // git' detection and activate maintainer-only regeneration rules
+        // (see is_vcs_dir_name). Removals land as whiteouts in the upper
+        // layer, leaving the lowerdir untouched.
+        if let Err(e) = super::prune_vcs_dirs(dest_path) {
+            log::warn!(
+                "Failed to prune VCS metadata from '{}': {}",
+                dest_path.display(),
+                e
+            );
+        }
+
         Ok(())
     }