Also, use genericArbitrary in Instances, this simplifies things

Also, some import refactoring

Previous to this commit, `get_user_root_node_folder` would fail with
a `UserHasTooManyRoots` in case this was called on a tree which had
more than one "public" folder.

We fix this by taking the oldest available node, which will always
correspond to the notion of "root", being the first ever created.

Ref: #238, #341, #418

Ref: #238, #341, #418

Also added a warning in `.ghci` in the form of a comment discouraging
people from overriding local REPL configuration options

This commit splits the policy checks we do on node operations into
"read" checks and "write" checks, so that we can enforce different kind
of policies based on the state of a node (i.e. published or not).

This commit refactors the `NodeNodeCategory` so that we create a better
hierarchy to account for node publication, including all the policies it
might have.

It also:

* Removes UserNodePublic from typesWhiteList in isNodeReadOnly

This commit refactors a bit the internal of the
`Gargantext.Database.Query.Tree` module so that it removes a lot of
repetitive boilerplate and paves the way to more interesting features.

It also:

* Adds the `isUserNode` boolean query
* Adjust source and target in publishNode and unpublishNode
* Pass the currently-logged-in user to tree API functions

It also:

* Amends tests for policy checks status code changes
* Fix a bug in isNodeReadOnly
* Adds a function to return all the nodes ids for the published
  nodes. Next we need to modify `findShared` & co to make sure that
  published notes will show somewhere in the users' tree.

Now this query accounts correctly for recursive children.

It also:

* Adds basic publish/unpublish works
* Add Move API tests scaffolding

Now a `NodeNodePoly` stores a typed `NodeNodeCategory`, we can use
to enforce invariants and making lookups more efficient.

This commit makes this function private to the `Table.NodeNode` module
as it's fairly low-level, and it doesn't let us embed logic to ensure we
are creating a valid node2node relationship. Better use one of the other
specialised functions.

This commit removes the `InsertDB` typeclass, an indirection which
wasn't very useful as it was being used in exactly one place in the
whole codebase (i.e. the share code).

Talking about share, this commit refactors things ever so slightly so
that we have a dedicated `shareNode` operation rather than using the
low-level `insertNodeNode`.

This commit splits the old `NodeAPIEndpoint` type into three;

* `NodeAPIEndpoint`, which will also contain the freeze endpoint;
* `AnnuaireAPIEndpoint`, which is the plain old node API without extra
  features;
* `CorpusAPIEndpoint`, which will also contain the publishin endpoint.

This split ensures that we don't add endpoints which do not belong to
all three categories, like before.

Furthermore this adds a public nodes SQL queries.
It also adds tests for getUserRootPublicNode

commit 0bbbba60
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Mon Nov 4 15:42:58 2024 +0100

    [VERSION] +1 to 0.0.7.3.6

commit 503f79e5
Merge: 7b630704 fff00f20
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Mon Nov 4 15:12:49 2024 +0100

    Merge remote-tracking branch 'origin/689-dev-graph-legend-show-all-clusters' into dev

commit 7b630704
Merge: c1eede02 c08eb0a0
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Mon Nov 4 15:12:31 2024 +0100

    Merge remote-tracking branch 'origin/adinapoli/issue-409' into dev

commit c08eb0a0
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 28 09:38:49 2024 +0100

    Fix Phylo golden tests for new field

commit 504b2514
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 28 08:48:22 2024 +0100

    Thread old compute time in flowPhyloAPI

    This allows us to collect a /history/ of computing times.

commit 7beb5d72
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Thu Oct 24 09:11:56 2024 +0200

    computeTime field in now optional

commit 2fd9c3e9
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Tue Oct 15 09:55:55 2024 +0200

    Add JSON roundtrip tests

commit 775aab73
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Tue Oct 15 09:21:49 2024 +0200

    Measure Phylo time via trackComputeTime

    The tracking is not perfect yet, as it keeps storing only the latest
    available compute time. Also, there seems to be some precision loss
    between that is reported by `timeMeasured` and what gets stored in the
    DB.

commit 41e31471
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 15:43:29 2024 +0200

    Add ComputeTimeHistory to Phylo type

commit fff00f20
Merge: 3da7a409 2df4c3bd
Author: Karen Konou <konoukaren@gmail.com>
Date:   Fri Oct 25 09:47:42 2024 +0200

    Merge branch 'dev' into 689-dev-graph-legend-show-all-clusters

commit c1eede02
Author: Przemysław Kaminski <pk@intrepidus.pl>
Date:   Fri Oct 18 12:46:13 2024 +0200

    [tests] fix notifications test

    This was because WS connection wasn't closed properly.

commit 2df4c3bd
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 24 13:59:06 2024 +0200

    [FIX] Module name

commit c9bea7e5
Merge: 9c2f627d 24a1767f
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Thu Oct 24 12:49:24 2024 +0200

    [Merge] Fix conflicts. I got error here at Test/API/Notifications.hs

commit 24a1767f
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Thu Oct 24 08:33:37 2024 +0200

    Fix TestName typo

commit 3b3fe772
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Thu Oct 24 08:33:15 2024 +0200

    Restore Phylo tests

commit 3da7a409
Author: Karen Konou <konoukaren@gmail.com>
Date:   Mon Oct 21 17:37:42 2024 +0200

    [Graph] Generate legend when computing graph

commit 3eebda86
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Wed Oct 23 10:24:18 2024 +0200

    Make Phylo tests using tasty-golden properly

commit 9c2f627d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Wed Oct 23 10:17:54 2024 +0200

    [VERSION] +1 to 0.0.7.3.5

commit 893b4cf8
Author: yacourt <acourt.yoelis@gmail.com>
Date:   Mon Oct 21 15:10:44 2024 +0200

    fix(ngrams): occurences counting with quotes

commit 2770f5e7
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Fri Oct 18 09:45:56 2024 +0200

    [VERSION] +1 to 0.0.7.3.4

commit 27413399
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 15 16:17:10 2024 +0200

    [VERSION] +1 to 0.0.7.3.3

commit f1d6a083
Merge: 0143f243 afdbe31d
Author: Alexandre Delanoë <devel+git@delanoe.org>
Date:   Tue Oct 15 15:45:40 2024 +0200

    Merge remote-tracking branch 'origin/improve-onboarding-experience' into dev

commit 0143f243
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 13:45:12 2024 +0200

    Fix step1c again

commit 43901901
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 12:39:43 2024 +0200

    Fix bug in GargPorter implementation

commit d44831d0
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 10:50:31 2024 +0200

    Introduce SpecContext, replicate search issue

    This commit refactors the test code ever so slightly to add a proper
    type called `SpecContext` rather than anonymous pairs to carry around
    the spec context/data. It also replicates the search problem around #415
    via a test.

commit b4260d9b
Author: Alfredo Di Napoli <alfredo.dinapoli@gmail.com>
Date:   Mon Oct 14 09:11:51 2024 +0200

    Add soysauce docs list to test-data

commit afdbe31d
Author: Grégoire Locqueville <gregoire.locqueville@cnrs.fr>
Date:   Thu Oct 10 18:51:46 2024 +0200

    Improve onboarding experience

    Edited the README to have a linear path to installation.
    Also made scripts to run the executables without having to worry
    whether they are on our path.

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