fix: remove gitignore negations that override fork protection (#796)

The negation patterns (!issues.jsonl, !interactions.jsonl, etc.) in
.beads/.gitignore had higher precedence than the fork protection
exclusion in .git/info/exclude, effectively defeating fork protection.

Contributors could accidentally stage and commit upstream issue
databases because:
1. Fork protection added .beads/issues.jsonl to .git/info/exclude
2. .beads/.gitignore had !issues.jsonl which overrode the exclusion
3. .gitignore files have higher precedence than .git/info/exclude

The negation patterns were unnecessary anyway since no pattern in
.beads/.gitignore matches those files. Added a comment explaining
why negations should not be added.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.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)
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
-!issues.jsonl
+# They would override fork protection in .git/info/exclude, allowing
-!interactions.jsonl
+# contributors to accidentally commit upstream issue databases.
-!metadata.json
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
-!config.json
+# are tracked by git by default since no pattern above ignores them.

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)
+# NOTE: Do NOT add negation patterns (e.g., !issues.jsonl) here.
-!issues.jsonl
+# They would override fork protection in .git/info/exclude, allowing
-!interactions.jsonl
+# contributors to accidentally commit upstream issue databases.
-!metadata.json
+# The JSONL files (issues.jsonl, interactions.jsonl) and config files
-!config.json
+# are tracked by git by default since no pattern above ignores them.
 `
 
 // requiredPatterns are patterns that MUST be in .beads/.gitignore

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) {