fix: prevent GitStore from creating nested repos and overwriting .gitignore (#2980)

GitStore.init() now checks if the workspace is already inside a git
repository before calling porcelain.init(). If so, it refuses to create
a nested repo. Additionally, existing .gitignore files are preserved
by appending only missing Dream-specific entries rather than overwriting.

Closes #2980

nanobot/utils/gitstore.py

@@ -64,14 +64,35 @@ class GitStore:
         if self.is_initialized():
             return False
 
+        if self._is_inside_git_repo():
+            logger.warning(
+                "Workspace {} is already inside a git repo; "
+                "skipping nested repo initialization",
+                self._workspace,
+            )
+            return False
+
         try:
             from dulwich import porcelain
 
             porcelain.init(str(self._workspace))
 
-            # Write .gitignore
+            # Write .gitignore (merge with existing if present)
             gitignore = self._workspace / ".gitignore"
-            gitignore.write_text(self._build_gitignore(), encoding="utf-8")
+            dream_entries = self._build_gitignore()
+            if gitignore.exists():
+                existing = gitignore.read_text(encoding="utf-8")
+                existing_lines = set(existing.splitlines())
+                new_lines = [
+                    line
+                    for line in dream_entries.splitlines()
+                    if line not in existing_lines
+                ]
+                if new_lines:
+                    merged = existing.rstrip("\n") + "\n" + "\n".join(new_lines) + "\n"
+                    gitignore.write_text(merged, encoding="utf-8")
+            else:
+                gitignore.write_text(dream_entries, encoding="utf-8")
 
             # Ensure tracked files exist (touch them if missing) so the initial
             # commit has something to track.
@@ -155,6 +176,19 @@ class GitStore:
         except Exception:
             return None
 
+    def _is_inside_git_repo(self) -> bool:
+        """Check if self._workspace is already inside a git repository.
+
+        Walks up from self._workspace to the filesystem root, returning True
+        if any parent directory contains a .git directory.
+        """
+        current = self._workspace.resolve()
+        while current != current.parent:
+            if (current / ".git").is_dir():
+                return True
+            current = current.parent
+        return False
+
     def _build_gitignore(self) -> str:
         """Generate .gitignore content from tracked files."""
         dirs: set[str] = set()