I can not confirm your issue/ When I run your sketch I see the seconds happily ticking away.
12:50:38.262 -> write compilationSep 21 202112:46:06
12:50:38.262 -> testsec: 0
12:50:38.262 -> hour 20
12:50:38.262 -> min 39
12:50:38.262 -> sec 0
12:50:38.262 ->
12:50:39.246 -> write compilationSep 21 202112:46:06
12:50:39.246 -> testsec: 1
12:50:39.246 -> hour 20
12:50:39.246 -> min 39
12:50:39.246 -> sec 0
12:50:39.246 ->
12:50:40.277 -> write compilationSep 21 202112:46:06
12:50:40.277 -> testsec: 2
12:50:40.277 -> hour 20
12:50:40.277 -> min 39
12:50:40.277 -> sec 0
12:50:40.277 ->
12:50:41.262 -> write compilationSep 21 202112:46:06
12:50:41.262 -> testsec: 3
12:50:41.262 -> hour 20
12:50:41.262 -> min 39
12:50:41.262 -> sec 0
12:50:41.262 ->
12:50:42.293 -> write compilationSep 21 202112:46:06
12:50:42.293 -> testsec: 4
12:50:42.293 -> hour 20
12:50:42.293 -> min 39
12:50:42.293 -> sec 0
12:50:42.293 ->
12:50:43.277 -> write compilationSep 21 202112:46:06
12:50:43.277 -> testsec: 5
If the clock halt bit were not set to 0, you would not be reading 0 for test seconds but rather 128, so I don't that that the oscillator not running due to clock halt bit is your issue.
Try running a basic library example for the ds1307.