fix: correct newline removal from fs_write and fs_patch

assets/functions/tools/fs_patch.sh

@@ -33,7 +33,11 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 # shellcheck disable=SC2154
 main() {
-    argc_contents="$(jq -r '.content' <<< "$LLM_TOOL_RAW_JSON")"
+		# Command substitution strips *all* trailing newlines and `jq -r` appends one
+		# of its own, so read with `-j` and pin the real end of the content with a
+		# sentinel that is removed afterwards.
+		argc_contents="$(jq -j '.content' <<< "$LLM_TOOL_RAW_JSON"; printf x)"
+		argc_contents="${argc_contents%x}"
     argc_path="$(jq -r '.path' <<< "$LLM_TOOL_RAW_JSON")"
 
     if [[ ! -f "$argc_path" ]]; then
@@ -41,7 +45,11 @@ main() {
         exit 1
     fi
 
-    new_contents="$(patch_file "$argc_path" <(printf "%s" "$argc_contents"))"
+		# Same sentinel guard on the patched result, otherwise the trailing newline
+		# is stripped again on the way back out. `rc` preserves patch_file's exit
+		# status so a failure still aborts under `set -e`.
+		new_contents="$(patch_file "$argc_path" <(printf "%s" "$argc_contents"); rc=$?; printf x; exit "$rc")"
+		new_contents="${new_contents%x}"
     printf "%s" "$new_contents" | git diff --no-index "$argc_path" - || true
 
     guard_operation "Apply changes?"

assets/functions/tools/fs_write.sh

@@ -15,7 +15,12 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 # shellcheck disable=SC2154
 main() {
-    argc_contents="$(jq -r '.content' <<< "$LLM_TOOL_RAW_JSON")"
+		# Command substitution strips *all* trailing newlines and `jq -r` appends one
+		# of its own, so read with `-j` and pin the real end of the content with a
+		# sentinel that is removed afterwards. Without this every written file loses
+		# its final newline, which breaks formatters such as `cargo fmt --check`.
+		argc_contents="$(jq -j '.content' <<< "$LLM_TOOL_RAW_JSON"; printf x)"
+		argc_contents="${argc_contents%x}"
     argc_path="$(jq -r '.path' <<< "$LLM_TOOL_RAW_JSON")"
 
     if [[ -f "$argc_path" ]]; then

src/rag/mod.rs

@@ -3044,7 +3044,7 @@ mod tests {
 
     #[test]
     fn reciprocal_rank_fusion_empty_lists() {
-        let result = super::reciprocal_rank_fusion(vec![], vec![], 5);
+        let result = reciprocal_rank_fusion(vec![], vec![], 5);
         assert!(result.is_empty(), "empty input should produce empty output");
     }
 
@@ -3052,7 +3052,7 @@ mod tests {
     fn reciprocal_rank_fusion_deduplicates_across_signals() {
         let doc_a = DocumentId::new(0, 0);
         let doc_b = DocumentId::new(0, 1);
-        let result = super::reciprocal_rank_fusion(
+        let result = reciprocal_rank_fusion(
             vec![vec![doc_a, doc_b], vec![doc_a, doc_b]],
             vec![1.0, 1.0],
             5,
@@ -3069,7 +3069,7 @@ mod tests {
     #[test]
     fn reciprocal_rank_fusion_respects_top_k() {
         let docs: Vec<DocumentId> = (0..10).map(|i| DocumentId::new(0, i)).collect();
-        let result = super::reciprocal_rank_fusion(vec![docs], vec![1.0], 3);
+        let result = reciprocal_rank_fusion(vec![docs], vec![1.0], 3);
         assert_eq!(result.len(), 3, "result should be capped at top_k=3");
     }
 
@@ -3077,7 +3077,7 @@ mod tests {
     fn reciprocal_rank_fusion_weights_affect_ranking() {
         let doc_a = DocumentId::new(0, 0);
         let doc_b = DocumentId::new(0, 1);
-        let result = super::reciprocal_rank_fusion(
+        let result = reciprocal_rank_fusion(
             vec![vec![doc_a, doc_b], vec![doc_b, doc_a]],
             vec![10.0, 1.0],
             2,