tests: try to make restored-datadir comparison tests not flaky (#6666)

This test occasionally fails with a difference in "pg_xact/0000" file
between the local and restored datadirs. My hypothesis is that something
changed in the database between the last explicit checkpoint and the
shutdown. I suspect autovacuum, it could certainly create transactions.

To fix, be more precise about the point in time that we compare. Shut
down the endpoint first, then read the last LSN (i.e. the shutdown
checkpoint's LSN), from the local disk with pg_controldata. And use
exactly that LSN in the basebackup.

Closes #559.

I'm proposing this as an alternative to
#6662.

test_runner/fixtures/neon_fixtures.py

@@ -3964,32 +3964,35 @@ def list_files_to_compare(pgdata_dir: Path) -> List[str]:
 
 # pg is the existing and running compute node, that we want to compare with a basebackup
 def check_restored_datadir_content(test_output_dir: Path, env: NeonEnv, endpoint: Endpoint):
+    pg_bin = PgBin(test_output_dir, env.pg_distrib_dir, env.pg_version)
+
     # Get the timeline ID. We need it for the 'basebackup' command
     timeline_id = TimelineId(endpoint.safe_psql("SHOW neon.timeline_id")[0][0])
 
-    # many tests already checkpoint, but do it just in case
-    with closing(endpoint.connect()) as conn:
-        with conn.cursor() as cur:
-            cur.execute("CHECKPOINT")
-
-    # wait for pageserver to catch up
-    wait_for_last_flush_lsn(env, endpoint, endpoint.tenant_id, timeline_id)
     # stop postgres to ensure that files won't change
     endpoint.stop()
 
+    # Read the shutdown checkpoint's LSN
+    pg_controldata_path = os.path.join(pg_bin.pg_bin_path, "pg_controldata")
+    cmd = f"{pg_controldata_path} -D {endpoint.pgdata_dir}"
+    result = subprocess.run(cmd, capture_output=True, text=True, shell=True)
+    checkpoint_lsn = re.findall(
+        "Latest checkpoint location:\\s+([0-9A-F]+/[0-9A-F]+)", result.stdout
+    )[0]
+    log.debug(f"last checkpoint at {checkpoint_lsn}")
+
     # Take a basebackup from pageserver
     restored_dir_path = env.repo_dir / f"{endpoint.endpoint_id}_restored_datadir"
     restored_dir_path.mkdir(exist_ok=True)
 
-    pg_bin = PgBin(test_output_dir, env.pg_distrib_dir, env.pg_version)
     psql_path = os.path.join(pg_bin.pg_bin_path, "psql")
 
     pageserver_id = env.attachment_service.locate(endpoint.tenant_id)[0]["node_id"]
     cmd = rf"""
         {psql_path}                                    \
             --no-psqlrc                                \
             postgres://localhost:{env.get_pageserver(pageserver_id).service_port.pg}  \
-            -c 'basebackup {endpoint.tenant_id} {timeline_id}'  \
+            -c 'basebackup {endpoint.tenant_id} {timeline_id} {checkpoint_lsn}'  \
          | tar -x -C {restored_dir_path}
     """