DB structure change + pending connection = bad sync

[wonder-sk]

There is a sync problem if the following conditions are met:

1. using WAL mode
2. user has modified structure of the geopackage file
3. there is a reader (or writer) connected to the file (could be a conn from GDAL conn pool)

When client tries to checkpoint the database, it will fail because of the other reader/writer - see (1, 4, 0) return value (the first value should be zero on success), keeping the original DB file unchanged, all changes stuck in the -wal file. Also create_changeset() fails, causing upload of the raw gpkg file (without changes) + update of basefile by file copy (also without changes). 🌩️

Condition 1 can be simulated like this:

    con = sqlite3.connect(test_gpkg)
    cursor = con.cursor()
    cursor.execute('CREATE TABLE test (fid SERIAL, txt TEXT);')
    cursor.execute('INSERT INTO test VALUES (123, \'hello\');')
    cursor.execute('COMMIT;')

Condition 2 can be simlated like this:

    con2 = sqlite3.connect(test_gpkg)
    cursor2 = con2.cursor()
    cursor2.execute('select count(*) from simple;')

A sample client log:

2021-05-28 23:39:18,889 --- start push martin/test_gpkg_change
2021-05-28 23:39:20,668 got project info: local version v1 / server version v1
2021-05-28 23:39:20,668 checkpoint - going to add it in /tmp/test_gpkg_change/test.gpkg
2021-05-28 23:39:25,679 checkpoint - return value: (1, 4, 0)
2021-05-28 23:39:25,693 checkpoint - new size 98304 checksum 6ff613aaf318f8e1bdeab6abb0d9a3848b43e2eb
2021-05-28 23:39:25,698 GEODIFF: Table names are not matching between the input databases.
Base:     simple
Modified: simple, test
2021-05-28 23:39:25,699 failed to create changeset for test.gpkg
2021-05-28 23:39:25,700 push changes:
{'added': [],
 'removed': [],
 'renamed': [],
 'updated': [{'checksum': '6ff613aaf318f8e1bdeab6abb0d9a3848b43e2eb',
              'chunks': ['86acddbd-9984-45ad-b8d7-f7108b0a9bc7'],
              'mtime': datetime.datetime(2021, 5, 28, 23, 39, 18, 758328, tzinfo=tzlocal()),
              'origin_checksum': '4e567044949c26899f10a9985b3f80b7e5477111',
              'path': 'test.gpkg',
              'size': 98304}]}
2021-05-28 23:39:28,125 got transaction ID 5773573e-14e4-4f07-a0aa-cd241cd91b76
2021-05-28 23:39:28,126 will upload 1 items with total size 98304
2021-05-28 23:39:28,129 Uploading /tmp/test_gpkg_change/test.gpkg part=0
2021-05-28 23:39:30,520 Upload finished: /tmp/test_gpkg_change/test.gpkg
2021-05-28 23:39:30,521 Finishing transaction 5773573e-14e4-4f07-a0aa-cd241cd91b76
2021-05-28 23:39:32,134 updating basefile (copy) for: test.gpkg
2021-05-28 23:39:32,134 --- push finished - new project version v2

[wonder-sk]

Fixed by #30 and verified with #100