chore: batch commit remaining changes

Includes search engine improvements, Alembic migrations,
new services (pubmed_daily_update, query_expansion),
frontend updates, and documentation sync.

ftp_test/check_file.py

@@ -0,0 +1,13 @@
+import gzip, io
+data = open('pubmed26n1546.xml.gz', 'rb').read()
+print(f'File size: {len(data)}')
+try:
+    decomp = gzip.decompress(data)
+    print(f'Valid gzip! Decompressed: {len(decomp)} bytes')
+    from lxml import etree
+    root = etree.parse(io.BytesIO(decomp)).getroot()
+    articles = root.findall('.//PubmedArticle')
+    deletes = root.findall('.//DeleteCitation')
+    print(f'PubmedArticle: {len(articles)}, DeleteCitation: {len(deletes)}')
+except Exception as e:
+    print(f'Corrupted: {e}')

ftp_test/download.py

@@ -0,0 +1,32 @@
+"""Download recent FTP update files for testing"""
+import ftplib, gzip, io, sys, time
+
+HOST = "ftp.ncbi.nlm.nih.gov"
+PATH = "/pubmed/updatefiles/"
+FILES = ["pubmed26n1544.xml.gz", "pubmed26n1545.xml.gz", "pubmed26n1546.xml.gz"]
+
+for name in FILES:
+    print(f"Downloading {name}...", end=" ", flush=True)
+    for attempt in range(3):
+        try:
+            ftp = ftplib.FTP(HOST, timeout=120)
+            ftp.login()
+            ftp.cwd(PATH)
+            buf = io.BytesIO()
+            ftp.retrbinary(f"RETR {name}", buf.write)
+            ftp.quit()
+            data = buf.getvalue()
+            # verify
+            gzip.decompress(data)
+            with open(name, "wb") as f:
+                f.write(data)
+            print(f"OK ({len(data)/1024/1024:.1f}MB)")
+            break
+        except Exception as e:
+            print(f"attempt {attempt+1} failed: {e}")
+            time.sleep(3)
+    else:
+        print("FAILED")
+        sys.exit(1)
+
+print("All files downloaded and verified successfully")

ftp_test/pubmed26n1544.xml.gz.md5

@@ -0,0 +1 @@
+MD5(pubmed26n1544.xml.gz)= 8fc6db055d14c130bb25b627d6f7ce93

ftp_test/pubmed26n1545.xml.gz.md5

@@ -0,0 +1 @@
+MD5(pubmed26n1545.xml.gz)= eb048ded970621df1cb89236878d0ee2

ftp_test/pubmed26n1546.xml.gz.md5

@@ -0,0 +1 @@
+MD5(pubmed26n1546.xml.gz)= d8866f67a94b52c079779d3111f76e05