This also changes the cabal.project to not pull the accelerate-llvm or
the llvm-hs dependencies.

It's crucial to be able to understand the API surface area when porting
the old code to `massiv`. It turns out that other than distributional,
the other piece of code using the LLVM interpreter is
`logDistributional2`.

The previous code was sometimes yielding a matrix of NaN numbers as
it was attempting the division of the input matrix with the diagonal,
which would be 0 in case of an input matrix of 0, resulting in a
division by 0 error.

- 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.

Also, fix for notifications throttle delay value

the 2A, which is my recommendation.

For some reasons that should be better analyzed, during the computation
of the Distributional similarity using Accelerate some parts of the
matrix are are below 1 (see the line modified by this commit). As a
consequence the log of such value below 1 gives a negative value that is
breaking the whole similarity computation: the matrix has negative and
non negative values and is becoming inconsistent.

The main fix consists in managing the values below 1 in order to get a
non negative matrix.

The Order 2A fixes the issue by adding 1 on each cell of the matrix.
The Order 2B fixes the issue by removing values below 1 only.

According to the qualitative tests I made the Graph results of order 2B
is better than the results of order 2A. Filtering seems better than
forcing using all data where some seems to be not "representative" enough.

Basically, Gargantext.Prelude exports all of Protolude now.

This fixes commit 5d5300cd which
automatically changed all 'return' to 'pure' in our code, resulting in
broken SQL etc.

They are changed to MaybeFields ...Read instead when joining.

Based on the suggestions in
https://kodimensional.dev/space-leak