Update mariadb and related components:

 - mariadb: 10.3.35 / 10.4.25 => 10.4.28
 - mroonga: 12.09 => 13.01
 - groonga: 12.0.7 => 13.0.1
 - groonga-normalizer-mysql: 1.1.8 => 1.2.1

Drop mariadb 10.3

---

Updating to 10.4 took time, because running the test from [`software/erp5/test/test/benchmarks.py`](https://lab.nexedi.com/nexedi/slapos/blob/c2e5a077453eea8fdff609d84d090fde40718bfc/software/erp5/test/test/benchmarks.py) sometimes caused mariadb to crash after some time - usually running the test 10 times in a loop was causing the crash (after 1 or 2 days).

Most of the time, mariadb process is still running, but no longer handle clients, gdb always showed a thread like this:

```
Thread 160 (Thread 0x7f15a505c700 (LWP 122797)):
#0  0x00007f1e0454771b in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#1  0x00007f1e044c5558 in malloc () from /lib/x86_64-linux-gnu/libc.so.6
#2  0x00007f1e04548432 in backtrace_symbols () from /lib/x86_64-linux-gnu/libc.so.6
#3  0x00007f1df4c8a7c4 in grn_ctx_log_back_trace_backtrace (level=GRN_LOG_ERROR, ctx=0x7f132014bbc0) at ctx.c:2141
#4  grn_ctx_log_back_trace (ctx=ctx@entry=0x7f132014bbc0, level=level@entry=GRN_LOG_ERROR) at ctx.c:2178
#5  0x00007f1df4dd2ce6 in grn_io_lock (ctx=ctx@entry=0x7f132014bbc0, io=0x7f1465bac4b0, timeout=<optimized out>) at io.c:1475
#6  0x00007f1df4db2fd3 in grn_ii_column_update (ctx=ctx@entry=0x7f132014bbc0, ii=ii@entry=0x7f1465a5d860, rid=62265, section=1, oldvalue=oldvalue@entry=0x7f15a5057fc0, newvalue=newvalue@entry=0x7f15a5058190, posting=0x0) at ii.c:8463
#7  0x00007f1df4c99248 in grn_obj_default_set_value_hook (ctx=ctx@entry=0x7f132014bbc0, nargs=nargs@entry=1, args=args@entry=0x7f15a5057f98, user_data=user_data@entry=0x7f15a5058020) at db.c:3564
#8  0x00007f1df4ca04ec in call_hook (flags=1, value=<optimized out>, id=62265, obj=<optimized out>, ctx=0x7f132014bbc0) at db.c:8013
#9  grn_obj_set_value_column_var_size (flags=1, value=0x0, id=62265, column=0x7f1465a5cb80, ctx=0x7f132014bbc0) at db.c:8133
#10 grn_obj_set_value (ctx=0x7f132014bbc0, obj=obj@entry=0x7f1465a5cb80, id=62265, value=value@entry=0x7f15a5058190, flags=flags@entry=1) at db.c:8267
#11 0x00007f1e0041cb2c in ha_mroonga::storage_write_row (this=0x7f132014a0d0, buf=0x7f1320174c00 "\376k\032\030") at ha_mroonga.cpp:7350
#12 0x000055f10715d2df in handler::ha_write_row (this=0x7f132014a0d0, buf=0x7f1320174c00 "\376k\032\030") at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/handler.cc:6791
#13 0x000055f106f2cd29 in write_record (thd=thd@entry=0x7f1320000c08, table=table@entry=0x7f13201492b8, info=info@entry=0x7f15a5059450) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_insert.cc:1752
#14 0x000055f106f337ea in mysql_insert (thd=thd@entry=0x7f1320000c08, table_list=<optimized out>, fields=..., values_list=..., update_fields=..., update_values=..., duplic=<optimized out>, ignore=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_insert.cc:1083
#15 0x000055f106f631e9 in mysql_execute_command (thd=0x7f1320000c08) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_parse.cc:4598
#16 0x000055f106f68089 in mysql_parse (thd=0x7f1320000c08, rawbuf=<optimized out>, length=120, parser_state=0x7f15a505b580, is_com_multi=<optimized out>, is_next_command=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_parse.cc:7995
#17 0x000055f106f6a525 in dispatch_command (command=COM_QUERY, thd=0x7f1320000c08, packet=<optimized out>, packet_length=<optimized out>, is_com_multi=<optimized out>, is_next_command=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_class.h:1201
#18 0x000055f106f6b965 in do_command (thd=0x7f1320000c08) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_parse.cc:1378
#19 0x000055f107051c1e in do_handle_one_connection (connect=connect@entry=0x55f10a4ff608) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_connect.cc:1420
#20 0x000055f107051cdd in handle_one_connection (arg=0x55f10a4ff608) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/978a7604a7585b1e57406d8c07e0bc55/.build/mariadb-10.4.25/sql/sql_connect.cc:1316
#21 0x00007f1e0491cfa3 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0
#22 0x00007f1e0453a4cf in clone () from /lib/x86_64-linux-gnu/libc.so.6
```

or similar, another example:

```
Thread 162 (Thread 0x7f082db7f700 (LWP 51130)):
#0  0x00007f11d10e171b in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#1  0x00007f11d105f1bb in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#2  0x00007f11d10a18ca in fork () from /lib/x86_64-linux-gnu/libc.so.6
#3  0x000055d4831dfd20 in start_addr2line_fork (binary_path=0x7ffcfa86ad29 "/srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/bin/mysqld") at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/mysys/my_addr_resolve.c:192
#4  start_addr2line_fork (binary_path=0x7ffcfa86ad29 "/srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/bin/mysqld") at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/mysys/my_addr_resolve.c:175
#5  0x000055d4831dfe54 in my_addr_resolve (ptr=0x55d4831c9fbe <my_print_stacktrace+46>, loc=loc@entry=0x7f082db7b600) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/mysys/my_addr_resolve.c:241
#6  0x000055d4831ca013 in print_with_addr_resolve (n=<optimized out>, addrs=0x7f082db7b620) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/mysys/stacktrace.c:159
#7  my_print_stacktrace (stack_bottom=<optimized out>, thread_stack=<optimized out>, silent=silent@entry=0 '\000') at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/mysys/stacktrace.c:178
#8  0x000055d482c9759d in handle_fatal_signal (sig=6) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/signal_handler.cc:231
#9  <signal handler called>
#10 0x00007f11d10127bb in raise () from /lib/x86_64-linux-gnu/libc.so.6
#11 0x00007f11d0ffd535 in abort () from /lib/x86_64-linux-gnu/libc.so.6
#12 0x00007f11d1054508 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#13 0x00007f11d105ac1a in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#14 0x00007f11d105c730 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#15 0x00007f11ccf95a0b in ha_mroonga::~ha_mroonga (this=0x7f06d818c960, __in_chrg=<optimized out>) at ha_mroonga.cpp:3185
#16 0x000055d482b63416 in closefrm (table=table@entry=0x7f06d8032ff8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/table.cc:4292
#17 0x000055d482c1e797 in intern_close_table (table=0x7f06d8032ff8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/table_cache.cc:221
#18 tc_remove_table (table=table@entry=0x7f06d8032ff8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/table_cache.cc:259
#19 0x000055d482c1ec13 in tc_release_table (table=0x7f06d8032ff8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/table_cache.cc:471
#20 0x000055d482a42842 in close_thread_table (thd=thd@entry=0x7f06d8000c08, table_ptr=table_ptr@entry=0x7f06d8000cf0) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_base.cc:1090
#21 0x000055d482a42a33 in close_thread_tables (thd=thd@entry=0x7f06d8000c08) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_base.cc:1030
#22 0x000055d482aa584b in mysql_execute_command (thd=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_parse.cc:6262
#23 0x000055d482aad1f9 in mysql_parse (thd=0x7f06d8000c08, rawbuf=<optimized out>, length=70, parser_state=0x7f082db7e550, is_com_multi=<optimized out>, is_next_command=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_parse.cc:7986
#24 0x000055d482aaf905 in dispatch_command (command=COM_QUERY, thd=0x7f06d8000c08, packet=<optimized out>, packet_length=<optimized out>, is_com_multi=<optimized out>, is_next_command=<optimized out>) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_class.h:1231
#25 0x000055d482ab0ad5 in do_command (thd=0x7f06d8000c08) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_parse.cc:1378
#26 0x000055d482b982be in do_handle_one_connection (connect=connect@entry=0x55d4b07df2f8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_connect.cc:1420
#27 0x000055d482b9837d in handle_one_connection (arg=0x55d4b07df2f8) at /srv/slapgrid/slappart15/srv/runner/instance/slappart7/tmp/shared/mariadb/bc5b4cdfa9be701b27f7ba3d46532f17/.build/mariadb-10.4.28/sql/sql_connect.cc:1324
#28 0x00007f11d14b6fa3 in start_thread () from /lib/x86_64-linux-gnu/libpthread.so.0
#29 0x00007f11d10d44cf in clone () from /lib/x86_64-linux-gnu/libc.so.6

```

On the machine used to reproduce this (COMP-3490), this reproduced for all combinations of mariadb/mroonga/groonga I tried, **even the versions that we are using in production without seeing this problem**, so my conclusions are that it should not be worse to use mariadb 10.4 regarding this problem.

See merge request !1364

see nexedi/cloudooo!32

See merge request nexedi/slapos!1394

See merge request nexedi/slapos!1402

If there has a stale postmaster.pid, it will be an error if we are
trying to connect the server. In this case, delete it and then start the
service again.

Without this fix, we cannot compile re6st-node because we don't use the
correct version of setuptools.

without the fix, we get this on Debian 12 compilation:

[2023-06-13 16:19:14,522] INFO     Cloning into '/opt/slapgrid/575c4158f610d2eb6886264b60654ce8/parts/shellinabox-git-repository'...
[2023-06-13 16:19:14,526] INFO     /opt/slapgrid/shared/git/e7d6bd941dfb709752c59e8f2a2b9127/libexec/git-core/git-remote-https: error while loading shared libraries: libcurl.so.4: cannot open shared object file: No such file or directory
[2023-06-13 16:19:14,551] INFO     While:
[2023-06-13 16:19:14,551] INFO       Installing shellinabox-git-repository.

See merge request nexedi/slapos!1401

  Update logs directive to set LogFormat properly

Also switch to basic authentication, this is generally more supported
than digest; keeweb for example only supports basic authentication. It
seems less secure though ( https://github.com/sigoden/dufs/issues/228 )

See merge request nexedi/slapos!1398

Since surykatka 0.8.0 the DB is not updated by default on elapsed time change,
and that shall be user explicit configuration. Thus fix
"software/monitor: Version up surykatka 0.8.0" by adding, required from
edgetest-basic perspective, switch ELAPSED_FAST.

neo logs to sqlite databases, not to "append only" files, so we need extra
care when rotation and cannot use the new "copytruncate" approach.

needs nexedi/erp5!1786

See merge request nexedi/slapos!1395

log files used by neo storage are not text files, they are sqlite
databases, so we can not use copytruncate because it leaves a broken
database. For neo, we have to go back to sending a SIGUSR1 signal to
tell neo client to reopen log files. This depends on neo registering
a signal handler, which is done in [1]. It depends on ZServer, so this
approach will probably have to be adjusted when running on python3
because the current plan is that we don't have ZServer installed on
python3.

This depends on a recent erp5.git where runwsgi understands --pidfile
argument.

1: https://lab.nexedi.com/nexedi/neoppod/blob/fd87e153/neo/client/app.py#L58

In 0409f691 (zope4: Handle log rotation following Zope documentation.,
2022-03-10) we added an option to use copytruncate in logrotate, with
a default value of "false" which is true in jinja2, so it was actually
enabled every where.

This change brings the expected behavior copytruncate option in
logrotate stack, it is not enabled by default, unless explicitly using
copytruncate = true

This can be helpful when comparing measurements or more generally when
trying multiple versions