diff --git a/.beads/.gitignore b/.beads/.gitignore
index 96620144..e68d2a20 100644
--- a/.beads/.gitignore
+++ b/.beads/.gitignore
@@ -27,8 +27,8 @@ beads.left.meta.json
 beads.right.jsonl
 beads.right.meta.json
 
-# Keep JSONL exports and config (source of truth for git)
-!issues.jsonl
-!interactions.jsonl
-!metadata.json
-!config.json
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
+# They would override fork protection in .git/info/exclude, allowing
+# contributors to accidentally commit upstream issue databases.
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
+# are tracked by git by default since no pattern above ignores them.
diff --git a/cmd/bd/doctor/gitignore.go b/cmd/bd/doctor/gitignore.go
index 8b141e9d..676447d8 100644
--- a/cmd/bd/doctor/gitignore.go
+++ b/cmd/bd/doctor/gitignore.go
@@ -36,11 +36,11 @@ beads.left.meta.json
 beads.right.jsonl
 beads.right.meta.json
 
-# Keep JSONL exports and config (source of truth for git)
-!issues.jsonl
-!interactions.jsonl
-!metadata.json
-!config.json
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
+# They would override fork protection in .git/info/exclude, allowing
+# contributors to accidentally commit upstream issue databases.
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
+# are tracked by git by default since no pattern above ignores them.
 `
 
 // requiredPatterns are patterns that MUST be in .beads/.gitignore
diff --git a/cmd/bd/init_test.go b/cmd/bd/init_test.go
index 4f81122e..e3de68a1 100644
--- a/cmd/bd/init_test.go
+++ b/cmd/bd/init_test.go
@@ -129,7 +129,7 @@ func TestInitCommand(t *testing.T) {
 					"beads.base.jsonl",
 					"beads.left.jsonl",
 					"beads.right.jsonl",
-					"!issues.jsonl",
+					"Do NOT add negation patterns", // Comment explaining fork protection
 				}
 				for _, pattern := range expectedPatterns {
 					if !strings.Contains(gitignoreStr, pattern) {