feat(xref): extract cross-references from descriptions, user notes, and fix system note regex

- Fix MENTIONED_RE/CLOSED_BY_RE to match real GitLab format
  ('mentioned in issue #N' / 'mentioned in merge request !N')
- Add GITLAB_URL_RE + parse_url_refs() for full URL extraction
- Add extract_refs_from_descriptions() -> source_method='description_parse'
- Add extract_refs_from_user_notes() -> source_method='note_parse'
- Wire both into orchestrator after system note extraction
- 36 tests: regex fix, URL parsing, integration, idempotency

src/core/note_parser_tests.rs

@@ -1,8 +1,10 @@
 use super::*;
 
+// --- parse_cross_refs: real GitLab system note format ---
+
 #[test]
 fn test_parse_mentioned_in_mr() {
-    let refs = parse_cross_refs("mentioned in !567");
+    let refs = parse_cross_refs("mentioned in merge request !567");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "mentioned");
     assert_eq!(refs[0].target_entity_type, "merge_request");
@@ -12,7 +14,7 @@ fn test_parse_mentioned_in_mr() {
 
 #[test]
 fn test_parse_mentioned_in_issue() {
-    let refs = parse_cross_refs("mentioned in #234");
+    let refs = parse_cross_refs("mentioned in issue #234");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "mentioned");
     assert_eq!(refs[0].target_entity_type, "issue");
@@ -22,7 +24,7 @@ fn test_parse_mentioned_in_issue() {
 
 #[test]
 fn test_parse_mentioned_cross_project() {
-    let refs = parse_cross_refs("mentioned in group/repo!789");
+    let refs = parse_cross_refs("mentioned in merge request group/repo!789");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "mentioned");
     assert_eq!(refs[0].target_entity_type, "merge_request");
@@ -32,7 +34,7 @@ fn test_parse_mentioned_cross_project() {
 
 #[test]
 fn test_parse_mentioned_cross_project_issue() {
-    let refs = parse_cross_refs("mentioned in group/repo#123");
+    let refs = parse_cross_refs("mentioned in issue group/repo#123");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "mentioned");
     assert_eq!(refs[0].target_entity_type, "issue");
@@ -42,7 +44,7 @@ fn test_parse_mentioned_cross_project_issue() {
 
 #[test]
 fn test_parse_closed_by_mr() {
-    let refs = parse_cross_refs("closed by !567");
+    let refs = parse_cross_refs("closed by merge request !567");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "closes");
     assert_eq!(refs[0].target_entity_type, "merge_request");
@@ -52,7 +54,7 @@ fn test_parse_closed_by_mr() {
 
 #[test]
 fn test_parse_closed_by_cross_project() {
-    let refs = parse_cross_refs("closed by group/repo!789");
+    let refs = parse_cross_refs("closed by merge request group/repo!789");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].reference_type, "closes");
     assert_eq!(refs[0].target_entity_type, "merge_request");
@@ -62,7 +64,7 @@ fn test_parse_closed_by_cross_project() {
 
 #[test]
 fn test_parse_multiple_refs() {
-    let refs = parse_cross_refs("mentioned in !123 and mentioned in #456");
+    let refs = parse_cross_refs("mentioned in merge request !123 and mentioned in issue #456");
     assert_eq!(refs.len(), 2);
     assert_eq!(refs[0].target_entity_type, "merge_request");
     assert_eq!(refs[0].target_iid, 123);
@@ -84,7 +86,7 @@ fn test_parse_non_english_note() {
 
 #[test]
 fn test_parse_multi_level_group_path() {
-    let refs = parse_cross_refs("mentioned in top/sub/project#123");
+    let refs = parse_cross_refs("mentioned in issue top/sub/project#123");
     assert_eq!(refs.len(), 1);
     assert_eq!(
         refs[0].target_project_path.as_deref(),
@@ -95,7 +97,7 @@ fn test_parse_multi_level_group_path() {
 
 #[test]
 fn test_parse_deeply_nested_group_path() {
-    let refs = parse_cross_refs("mentioned in a/b/c/d/e!42");
+    let refs = parse_cross_refs("mentioned in merge request a/b/c/d/e!42");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].target_project_path.as_deref(), Some("a/b/c/d/e"));
     assert_eq!(refs[0].target_iid, 42);
@@ -103,7 +105,7 @@ fn test_parse_deeply_nested_group_path() {
 
 #[test]
 fn test_parse_hyphenated_project_path() {
-    let refs = parse_cross_refs("mentioned in my-group/my-project#99");
+    let refs = parse_cross_refs("mentioned in issue my-group/my-project#99");
     assert_eq!(refs.len(), 1);
     assert_eq!(
         refs[0].target_project_path.as_deref(),
@@ -113,7 +115,7 @@ fn test_parse_hyphenated_project_path() {
 
 #[test]
 fn test_parse_dotted_project_path() {
-    let refs = parse_cross_refs("mentioned in visiostack.io/backend#123");
+    let refs = parse_cross_refs("mentioned in issue visiostack.io/backend#123");
     assert_eq!(refs.len(), 1);
     assert_eq!(
         refs[0].target_project_path.as_deref(),
@@ -124,7 +126,7 @@ fn test_parse_dotted_project_path() {
 
 #[test]
 fn test_parse_dotted_nested_project_path() {
-    let refs = parse_cross_refs("closed by my.org/sub.group/my.project!42");
+    let refs = parse_cross_refs("closed by merge request my.org/sub.group/my.project!42");
     assert_eq!(refs.len(), 1);
     assert_eq!(
         refs[0].target_project_path.as_deref(),
@@ -134,16 +136,27 @@ fn test_parse_dotted_nested_project_path() {
     assert_eq!(refs[0].target_iid, 42);
 }
 
+// Bare-sigil fallback (no "issue"/"merge request" word) still works
 #[test]
-fn test_parse_self_reference_is_valid() {
+fn test_parse_bare_sigil_fallback() {
     let refs = parse_cross_refs("mentioned in #123");
     assert_eq!(refs.len(), 1);
     assert_eq!(refs[0].target_iid, 123);
+    assert_eq!(refs[0].target_entity_type, "issue");
+}
+
+#[test]
+fn test_parse_bare_sigil_closed_by() {
+    let refs = parse_cross_refs("closed by !567");
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].reference_type, "closes");
+    assert_eq!(refs[0].target_entity_type, "merge_request");
+    assert_eq!(refs[0].target_iid, 567);
 }
 
 #[test]
 fn test_parse_mixed_mentioned_and_closed() {
-    let refs = parse_cross_refs("mentioned in !10 and closed by !20");
+    let refs = parse_cross_refs("mentioned in merge request !10 and closed by merge request !20");
     assert_eq!(refs.len(), 2);
     assert_eq!(refs[0].reference_type, "mentioned");
     assert_eq!(refs[0].target_iid, 10);
@@ -151,6 +164,113 @@ fn test_parse_mixed_mentioned_and_closed() {
     assert_eq!(refs[1].target_iid, 20);
 }
 
+// --- parse_url_refs ---
+
+#[test]
+fn test_url_ref_same_project_issue() {
+    let refs = parse_url_refs(
+        "See https://gitlab.visiostack.com/vs/typescript-code/-/issues/3537 for details",
+    );
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].target_entity_type, "issue");
+    assert_eq!(refs[0].target_iid, 3537);
+    assert_eq!(
+        refs[0].target_project_path.as_deref(),
+        Some("vs/typescript-code")
+    );
+    assert_eq!(refs[0].reference_type, "mentioned");
+}
+
+#[test]
+fn test_url_ref_merge_request() {
+    let refs =
+        parse_url_refs("https://gitlab.visiostack.com/vs/typescript-code/-/merge_requests/3548");
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].target_entity_type, "merge_request");
+    assert_eq!(refs[0].target_iid, 3548);
+    assert_eq!(
+        refs[0].target_project_path.as_deref(),
+        Some("vs/typescript-code")
+    );
+}
+
+#[test]
+fn test_url_ref_cross_project() {
+    let refs = parse_url_refs(
+        "Related: https://gitlab.visiostack.com/vs/python-code/-/merge_requests/5203",
+    );
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].target_entity_type, "merge_request");
+    assert_eq!(refs[0].target_iid, 5203);
+    assert_eq!(
+        refs[0].target_project_path.as_deref(),
+        Some("vs/python-code")
+    );
+}
+
+#[test]
+fn test_url_ref_with_anchor() {
+    let refs =
+        parse_url_refs("https://gitlab.visiostack.com/vs/typescript-code/-/issues/123#note_456");
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].target_entity_type, "issue");
+    assert_eq!(refs[0].target_iid, 123);
+}
+
+#[test]
+fn test_url_ref_markdown_link() {
+    let refs = parse_url_refs(
+        "Check [this MR](https://gitlab.visiostack.com/vs/typescript-code/-/merge_requests/100) for context",
+    );
+    assert_eq!(refs.len(), 1);
+    assert_eq!(refs[0].target_entity_type, "merge_request");
+    assert_eq!(refs[0].target_iid, 100);
+}
+
+#[test]
+fn test_url_ref_multiple_urls() {
+    let body =
+        "See https://gitlab.com/a/b/-/issues/1 and https://gitlab.com/a/b/-/merge_requests/2";
+    let refs = parse_url_refs(body);
+    assert_eq!(refs.len(), 2);
+    assert_eq!(refs[0].target_entity_type, "issue");
+    assert_eq!(refs[0].target_iid, 1);
+    assert_eq!(refs[1].target_entity_type, "merge_request");
+    assert_eq!(refs[1].target_iid, 2);
+}
+
+#[test]
+fn test_url_ref_deduplicates() {
+    let body = "See https://gitlab.com/a/b/-/issues/1 and again https://gitlab.com/a/b/-/issues/1";
+    let refs = parse_url_refs(body);
+    assert_eq!(
+        refs.len(),
+        1,
+        "Duplicate URLs in same body should be deduplicated"
+    );
+}
+
+#[test]
+fn test_url_ref_non_gitlab_urls_ignored() {
+    let refs = parse_url_refs(
+        "Check https://google.com/search?q=test and https://github.com/org/repo/issues/1",
+    );
+    assert!(refs.is_empty());
+}
+
+#[test]
+fn test_url_ref_deeply_nested_project() {
+    let refs = parse_url_refs("https://gitlab.com/org/sub/deep/project/-/issues/42");
+    assert_eq!(refs.len(), 1);
+    assert_eq!(
+        refs[0].target_project_path.as_deref(),
+        Some("org/sub/deep/project")
+    );
+    assert_eq!(refs[0].target_iid, 42);
+}
+
+// --- Integration tests: system notes (updated for real format) ---
+
 fn setup_test_db() -> Connection {
     use crate::core::db::{create_connection, run_migrations};
 
@@ -204,27 +324,31 @@ fn seed_test_data(conn: &Connection) -> i64 {
     )
     .unwrap();
 
+    // System note: real GitLab format "mentioned in merge request !789"
     conn.execute(
         "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
-         VALUES (40, 4000, 30, 1, 1, 'mentioned in !789', ?1, ?1, ?1)",
+         VALUES (40, 4000, 30, 1, 1, 'mentioned in merge request !789', ?1, ?1, ?1)",
         [now],
     )
     .unwrap();
 
+    // System note: real GitLab format "mentioned in issue #456"
     conn.execute(
         "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
-         VALUES (41, 4001, 31, 1, 1, 'mentioned in #456', ?1, ?1, ?1)",
+         VALUES (41, 4001, 31, 1, 1, 'mentioned in issue #456', ?1, ?1, ?1)",
         [now],
     )
     .unwrap();
 
+    // User note (is_system=0) — should NOT be processed by system note extractor
     conn.execute(
         "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
-         VALUES (42, 4002, 30, 1, 0, 'mentioned in !999', ?1, ?1, ?1)",
+         VALUES (42, 4002, 30, 1, 0, 'mentioned in merge request !999', ?1, ?1, ?1)",
         [now],
     )
     .unwrap();
 
+    // System note with no cross-ref pattern
     conn.execute(
         "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
          VALUES (43, 4003, 30, 1, 1, 'added label ~bug', ?1, ?1, ?1)",
@@ -232,9 +356,10 @@ fn seed_test_data(conn: &Connection) -> i64 {
     )
     .unwrap();
 
+    // System note: cross-project ref
     conn.execute(
         "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
-         VALUES (44, 4004, 30, 1, 1, 'mentioned in other/project#999', ?1, ?1, ?1)",
+         VALUES (44, 4004, 30, 1, 1, 'mentioned in issue other/project#999', ?1, ?1, ?1)",
         [now],
     )
     .unwrap();
@@ -323,3 +448,323 @@ fn test_extract_refs_empty_project() {
     assert_eq!(result.skipped_unresolvable, 0);
     assert_eq!(result.parse_failures, 0);
 }
+
+// --- Integration tests: description extraction ---
+
+#[test]
+fn test_extract_refs_from_descriptions_issue() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/typescript-code', 'https://gitlab.com/vs/typescript-code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    // Issue with MR reference in description
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, description, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 3537, 'Test Issue', 'opened',
+                 'Related to https://gitlab.com/vs/typescript-code/-/merge_requests/3548',
+                 ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    // The target MR so it resolves
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 3548, 'Fix MR', 'merged', 'fix', 'main', 'dev', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let result = extract_refs_from_descriptions(&conn, 1).unwrap();
+
+    assert_eq!(result.inserted, 1, "Should insert 1 description ref");
+    assert_eq!(result.skipped_unresolvable, 0);
+
+    let method: String = conn
+        .query_row(
+            "SELECT source_method FROM entity_references WHERE project_id = 1",
+            [],
+            |row| row.get(0),
+        )
+        .unwrap();
+    assert_eq!(method, "description_parse");
+}
+
+#[test]
+fn test_extract_refs_from_descriptions_mr() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/typescript-code', 'https://gitlab.com/vs/typescript-code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 100, 'Target Issue', 'opened', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, description, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 200, 'Fixing MR', 'merged', 'fix', 'main', 'dev',
+                 'Fixes https://gitlab.com/vs/typescript-code/-/issues/100',
+                 ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let result = extract_refs_from_descriptions(&conn, 1).unwrap();
+
+    assert_eq!(result.inserted, 1);
+
+    let (src_type, tgt_type): (String, String) = conn
+        .query_row(
+            "SELECT source_entity_type, target_entity_type FROM entity_references WHERE project_id = 1",
+            [],
+            |row| Ok((row.get(0)?, row.get(1)?)),
+        )
+        .unwrap();
+    assert_eq!(src_type, "merge_request");
+    assert_eq!(tgt_type, "issue");
+}
+
+#[test]
+fn test_extract_refs_from_descriptions_idempotent() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/code', 'https://gitlab.com/vs/code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, description, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 1, 'Issue', 'opened',
+                 'See https://gitlab.com/vs/code/-/merge_requests/2', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 2, 'MR', 'opened', 'x', 'main', 'dev', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let r1 = extract_refs_from_descriptions(&conn, 1).unwrap();
+    assert_eq!(r1.inserted, 1);
+
+    let r2 = extract_refs_from_descriptions(&conn, 1).unwrap();
+    assert_eq!(r2.inserted, 0, "Second run should insert 0 (idempotent)");
+}
+
+#[test]
+fn test_extract_refs_from_descriptions_cross_project_unresolved() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/typescript-code', 'https://gitlab.com/vs/typescript-code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, description, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 1, 'Issue', 'opened',
+                 'See https://gitlab.com/vs/other-project/-/merge_requests/99', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let result = extract_refs_from_descriptions(&conn, 1).unwrap();
+
+    assert_eq!(result.inserted, 0);
+    assert_eq!(
+        result.skipped_unresolvable, 1,
+        "Cross-project ref with no matching project should be unresolvable"
+    );
+
+    let (path, iid): (String, i64) = conn
+        .query_row(
+            "SELECT target_project_path, target_entity_iid FROM entity_references WHERE target_entity_id IS NULL",
+            [],
+            |row| Ok((row.get(0)?, row.get(1)?)),
+        )
+        .unwrap();
+    assert_eq!(path, "vs/other-project");
+    assert_eq!(iid, 99);
+}
+
+// --- Integration tests: user note extraction ---
+
+#[test]
+fn test_extract_refs_from_user_notes_with_url() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/code', 'https://gitlab.com/vs/code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 50, 'Source Issue', 'opened', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 60, 'Target MR', 'opened', 'x', 'main', 'dev', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO discussions (id, gitlab_discussion_id, project_id, issue_id, noteable_type, last_seen_at)
+         VALUES (30, 'disc-user', 1, 10, 'Issue', ?1)",
+        [now],
+    )
+    .unwrap();
+
+    // User note with a URL
+    conn.execute(
+        "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
+         VALUES (40, 4000, 30, 1, 0,
+                 'This is related to https://gitlab.com/vs/code/-/merge_requests/60',
+                 ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let result = extract_refs_from_user_notes(&conn, 1).unwrap();
+
+    assert_eq!(result.inserted, 1);
+
+    let method: String = conn
+        .query_row(
+            "SELECT source_method FROM entity_references WHERE project_id = 1",
+            [],
+            |row| row.get(0),
+        )
+        .unwrap();
+    assert_eq!(method, "note_parse");
+}
+
+#[test]
+fn test_extract_refs_from_user_notes_no_system_note_patterns() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/code', 'https://gitlab.com/vs/code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 50, 'Source', 'opened', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 999, 'Target', 'opened', 'x', 'main', 'dev', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO discussions (id, gitlab_discussion_id, project_id, issue_id, noteable_type, last_seen_at)
+         VALUES (30, 'disc-x', 1, 10, 'Issue', ?1)",
+        [now],
+    )
+    .unwrap();
+
+    // User note with system-note-like text but no URL — should NOT extract
+    // (user notes only use URL parsing, not system note pattern matching)
+    conn.execute(
+        "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
+         VALUES (40, 4000, 30, 1, 0, 'mentioned in merge request !999', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let result = extract_refs_from_user_notes(&conn, 1).unwrap();
+
+    assert_eq!(
+        result.inserted, 0,
+        "User notes should only parse URLs, not system note patterns"
+    );
+}
+
+#[test]
+fn test_extract_refs_from_user_notes_idempotent() {
+    let conn = setup_test_db();
+    let now = now_ms();
+
+    conn.execute(
+        "INSERT INTO projects (id, gitlab_project_id, path_with_namespace, web_url, created_at, updated_at)
+         VALUES (1, 100, 'vs/code', 'https://gitlab.com/vs/code', ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO issues (id, gitlab_id, project_id, iid, title, state, created_at, updated_at, last_seen_at)
+         VALUES (10, 1000, 1, 1, 'Src', 'opened', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO merge_requests (id, gitlab_id, project_id, iid, title, state, source_branch, target_branch, author_username, created_at, updated_at, last_seen_at)
+         VALUES (20, 2000, 1, 2, 'Tgt', 'opened', 'x', 'main', 'dev', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO discussions (id, gitlab_discussion_id, project_id, issue_id, noteable_type, last_seen_at)
+         VALUES (30, 'disc-y', 1, 10, 'Issue', ?1)",
+        [now],
+    )
+    .unwrap();
+
+    conn.execute(
+        "INSERT INTO notes (id, gitlab_id, discussion_id, project_id, is_system, body, created_at, updated_at, last_seen_at)
+         VALUES (40, 4000, 30, 1, 0,
+                 'See https://gitlab.com/vs/code/-/merge_requests/2', ?1, ?1, ?1)",
+        [now],
+    )
+    .unwrap();
+
+    let r1 = extract_refs_from_user_notes(&conn, 1).unwrap();
+    assert_eq!(r1.inserted, 1);
+
+    let r2 = extract_refs_from_user_notes(&conn, 1).unwrap();
+    assert_eq!(r2.inserted, 0, "Second extraction should be idempotent");
+}