This gigantic commit ports the existing DB operations in GGTX to use the
transactional API, meaning that we can now compose DB operations and
they will all run in the same Postgres transaction using the same
connection, which will eliminate those class of bugs where concurrent DB
access might result in an inconsistent state.

On top of that, we simplify some parts of the API, for which a summary
is given below:

1. The `NodeStoryEnv` management has been greatly simplified; in the new
   API we don't need an external connection pool to be passed and we
   don't have to pass IO actions, we can just pass DB operations,
   therefore we can greatly simplify the API to just pass mostly pure
   values;

2. Due to the fact that our `DBTx` monad can't do arbitrary IO (which is
   a good thing) we cannot fire Central Exchange notifications
   immediately. Rather that happens now is that we collect the
   `CEMessage` to be sent and we fire them in the relevant concrete
   monad after we finished with the DB transaction. This means that in
   principle there would be a small delay between the DB operation
   taking place and the notification firing but in practice the latency
   should be negligible and bear in mind this is typically what we want:
   if we have a long DB Tx that triggers an error in the middle we don't
   want to be sending out CE messages prematurely if the overall
   operation didn't succeed!

3. There are still a few places in the codebase where we couldn't make
   things fully compositional with regards to the DBTx API, because we
   had Servant handlers which had DB operations mixed with other IO
   effectful computations (or other things like the notification from
   the `MonadJobStatus`). For now we are splitting these functions by
   manually running the partial DB operations, and while this is not
   ideal it can be fixed in subsequent merge requests.

4. The `WorkerEnv` doesn't use `IOException` as its `MonadError`
   anymore, as for consistency we can just use `BackendInternalError` by
   adding a `InternalWorkerError` data constructor accepting the
   `IOException` triggered by the Worker monad.

More testing is needed, with particular attention to performance
(regression) but this should hopefully offer a decent baseline.

Also, some import refactoring

Also, removed some old job stuff

commit 3030272d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 18:31:19 2024 +0200

    [VERSION] +1 to 0.0.7.3.2

commit bd33dd6c
Merge: 1d3417d9 592d966c
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 18:10:51 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit 592d966c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Oct 10 18:06:20 2024 +0200

    [notifications] add missing test/Test/Core/Notifications.hs

commit 1d3417d9
Merge: 163304df a48fe0c8
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 10 17:54:39 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit a48fe0c8
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Thu Oct 10 10:01:10 2024 +0200

    [ws] rename AsyncUpdates to Notifications

    This is bit more clear

commit cd831db4
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 16:00:48 2024 +0200

    [tests] first working notification test

commit 81af005d
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 11:05:11 2024 +0200

    Squashed commit of the following:

    commit 163304df
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:39:54 2024 +0200

        [FIX] conflict

    commit 82c68074
    Merge: f7b76918 5623161c
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:28:55 2024 +0200

        Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

    commit f7b76918
    Merge: fe7a92cc 88655f68
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 18:28:53 2024 +0200

        [FIX] conflicts

    commit fe7a92cc
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 17:19:53 2024 +0200

        fix: no longer update graphs and phylos on corpus update

    commit f775d4a3
    Merge: 76b557ea d2f4b89d
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:53 2024 +0200

        Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

    commit 76b557ea
    Merge: 2925d008 50c77ea2
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:27 2024 +0200

        Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

    commit d2f4b89d
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:37:54 2024 +0200

        DEVELOPER_GUIDELINES: update about git amend

        This is the result of Autumn workshop 2024

    commit 50c77ea2
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:15:28 2024 +0200

        [notifications] fix for send

        sendNonblocking threw an error initially. I just do a compromise and
        timeout the normal send (which blocks infinitely sometimes)

    commit 025b80b6
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 14:10:56 2024 +0200

        [docker] fix network: host, fix caddyfile

    commit 2925d008
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:34:17 2024 +0200

        fix arbitrary instance

    commit e8fb3db6
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:13:40 2024 +0200

        fix: re-add lost instances

    commit b86d2e61
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 10:09:18 2024 +0200

        [toml] remove pubmed api key from config

        It's set up in user settings instead and has been for a long time.

    commit c06de5ef
    Merge: ab710337 a0ec337b
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 09:35:55 2024 +0200

        Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

    commit ab710337
    Author: Christian Merten <christian@merten.dev>
    Date:   Fri Apr 26 22:32:33 2024 +0200

        feat: update corpus endpoint

commit d4a9200e
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Wed Oct 9 11:01:43 2024 +0200

    [ws] notification action on node share

commit 163304df
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:39:54 2024 +0200

    [FIX] conflict

commit 82c68074
Merge: f7b76918 5623161c
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:28:55 2024 +0200

    Merge remote-tracking branch 'origin/dev-websockets-node-update' into dev

commit f7b76918
Merge: fe7a92cc 88655f68
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 18:28:53 2024 +0200

    [FIX] conflicts

commit 5623161c
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 18:18:23 2024 +0200

    [ws] implement node update (rename, move) with notifications to parents

commit 88655f68
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 18:05:25 2024 +0200

    Squashed commit of the following:

    commit f775d4a3
    Merge: 76b557ea d2f4b89d
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:53 2024 +0200

        Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

    commit 76b557ea
    Merge: 2925d008 50c77ea2
    Author: Alexandre Delanoë <devel+git@delanoe.org>
    Date:   Tue Oct 8 16:27:27 2024 +0200

        Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

    commit d2f4b89d
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:37:54 2024 +0200

        DEVELOPER_GUIDELINES: update about git amend

        This is the result of Autumn workshop 2024

    commit 50c77ea2
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 15:15:28 2024 +0200

        [notifications] fix for send

        sendNonblocking threw an error initially. I just do a compromise and
        timeout the normal send (which blocks infinitely sometimes)

    commit 025b80b6
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 14:10:56 2024 +0200

        [docker] fix network: host, fix caddyfile

    commit 2925d008
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:34:17 2024 +0200

        fix arbitrary instance

    commit e8fb3db6
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 10:13:40 2024 +0200

        fix: re-add lost instances

    commit b86d2e61
    Author: Przemysław Kaminski <pk@intrepidus.pl>
    Date:   Tue Oct 8 10:09:18 2024 +0200

        [toml] remove pubmed api key from config

        It's set up in user settings instead and has been for a long time.

    commit c06de5ef
    Merge: ab710337 a0ec337b
    Author: Christian Merten <christian@merten.dev>
    Date:   Tue Oct 8 09:35:55 2024 +0200

        Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

    commit ab710337
    Author: Christian Merten <christian@merten.dev>
    Date:   Fri Apr 26 22:32:33 2024 +0200

        feat: update corpus endpoint

commit fe7a92cc
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 17:19:53 2024 +0200

    fix: no longer update graphs and phylos on corpus update

commit f775d4a3
Merge: 76b557ea d2f4b89d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 16:27:53 2024 +0200

    Merge remote-tracking branch 'origin/dev-guidelines-update' into dev

commit 76b557ea
Merge: 2925d008 50c77ea2
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 8 16:27:27 2024 +0200

    Merge remote-tracking branch 'origin/304-dev-pubmed-api-not-in-toml' into dev

commit d2f4b89d
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 15:37:54 2024 +0200

    DEVELOPER_GUIDELINES: update about git amend

    This is the result of Autumn workshop 2024

commit 50c77ea2
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 15:15:28 2024 +0200

    [notifications] fix for send

    sendNonblocking threw an error initially. I just do a compromise and
    timeout the normal send (which blocks infinitely sometimes)

commit 025b80b6
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 14:10:56 2024 +0200

    [docker] fix network: host, fix caddyfile

commit ee0db8c1
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 12:39:12 2024 +0200

    [nix] add nanomsg to nix pkgs

    Also, fix ./start to use gargantext-settings.toml

commit 2925d008
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 10:34:17 2024 +0200

    fix arbitrary instance

commit e8fb3db6
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 10:13:40 2024 +0200

    fix: re-add lost instances

commit b86d2e61
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Tue Oct 8 10:09:18 2024 +0200

    [toml] remove pubmed api key from config

    It's set up in user settings instead and has been for a long time.

commit c06de5ef
Merge: ab710337 a0ec337b
Author: Christian Merten <christian@merten.dev>
Date:   Tue Oct 8 09:35:55 2024 +0200

    Merge remote-tracking branch 'gitlab/dev' into cm/update-corpus-button

commit ab710337
Author: Christian Merten <christian@merten.dev>
Date:   Fri Apr 26 22:32:33 2024 +0200

    feat: update corpus endpoint

This is bit more clear

Now everything is in Core/Config

- Re-enable orphan warnings that were manually disabled in many modules
- Remove non-Haskell files that were just sitting in the source tree
- Remove modules that were not called from anywhere
- Remove unused dependencies

This is not exhaustive by any means. In particular, some more weeding out
can be achieved by looking at individual functions and even branches of
functions. Weeder can help with that.

This big commit ties the knot with the named _routes_ by providing
concrete server (i.e. handlers) implementations.

This is a first stepping stone in avoiding bugs by having `UserId` and
`ContextId` being proper types, and not synonyms.

We also refactor things to have `AuthenticatedUser` carry the `UserId`.

Basically, Gargantext.Prelude exports all of Protolude now.

This big commit improves the jobs API in a way that now we can
completely abstract away over a JobLog.

This works now for arbitrary nodes, irrespective of their type.