Added Laurent Turpin to the list of major contributors to
Aevol source code.

Update the indications in the README file to somehow help
new user get Aevol compiled and started. This is certainly
not a full guide, but hopefully a collection of clues.

Added Marco Foley and Théotime Grohens to the list of major
contributors to Aevol source code.

The autotools have previously been removed from the Aevol
build chain in favor of CMake. This commit removes git
ignore rules that dealt with in source build and autotools
generated files.

[DnaReplicationReport] Factor the loops over the 3 mutation types

See merge request aevol/aevol!32

Throughout the post-treatments, there is a pattern to iterate over all
mutations contained in the DnaReplicationReport of individuals.

As these are split into 3 std::lists of different types, the body of the
loop is usually repeated 3 times (once for each list), which is prone to
mistakes and hard to update if we want to add a new mutation type.

This commit factors this code by introducing a higher-order template
method named DnaReplicationReport::iter_muts(f), which takes a function
f and runs f(mut) for all mutations mut in the 3 lists.

This replaces the existing code very easily by turning the loop bodies
into a single lambda block, and allows us to change the code in one
single place (iter_muts()) if we want to introduce more mutation types.

Moreover, as the function iter_muts is compiled once for each call with a
different function f, and can be inlined, there should be no performance hit
compared to the original loops.

With clones, the individual id is not injective or surjective anymore.
Hence, a call to indiv_by_id() can return nullptr even for suspectedly
valid ids. This was the cause for a bug in the lineage post-treatment.

This commit therefore disables this method to avoid such problems.

[ExpManager] check_simd (allowing to verify Aevol 6 results against Aevol 7) should be desactivated by default

[RAevol7] Rename basic_stdlist example to basic (Aevol) and add a complex dynamic environment (Raevol)

Else both code (6 and 7) are running and checking each other.
Accordingly, everything is computed twice.

Seems to fix last memory leak

When running the `aevol_post_lineage` post-treatment, individuals
generated by ReplicationReports are periodically checked against
individuals recovered from backups to make sure everything is in order.

Up until now, these backed-up individuals were loaded with the
ExpManager::indiv_by_id() method. However, as clones can share the same
id, this method no longer works and should not be called anymore (and is
to be removed later on).

This commit addresses this by correctly loading the individual with the
World::indiv_at() method, which takes the x and y coordinates instead of
the id.

It was not used and the performance was too poor

This commit updates the Utils::PrintAevolVersion() method to use the
detailed version string provided in aevol::version_string.

This commit adds the build type (Release or Debug) to the detailed commit
info introduced in ee8f2200, in order to simplify later extraction of
this data from the output.

It is obtained by printing the $CMAKE_BUILD_TYPE CMake variable.

[aevol] Print compile commit branch, hash and date

See merge request aevol/aevol!30

This commit adds the ability to get the branch, date and hash of the
commit that was used to compile Aevol from within the C++ source of Aevol.

This is useful because it allows us to print it (for example) at the
beginning of the execution of one of the Aevol programs, making it
easier to see whether we're running the right version.

In order to do this, a special file `aevol_version.cpp.in` is introduced.
This file is modified by CMake a first time at configure time, replacing
a placeholder with the value of the PROJECT_VERSION CMake variable, and
a second time at compile time, replacing a placeholder with a custom
CMake variable that holds the branch, hash and date.

This turns the file into a regular C++ source file, that is then compiled
and linked with the rest of Aevol through the `aevol_version.h` header.

Finally, we print this string in the two most commonly used Aevol
executables, `aevol_create` and `aevol_run`.

[IOJson.cpp] W_max parameter correctly implemented

See merge request aevol/aevol!29

Import neutral mutations experiments post treatement

See merge request aevol/aevol!28

names of files depend on input file name and seed of simulation

[aevol_post_change_size_neutral_mut.cpp] output file individual has now the genetique sequence of the last individual of the post treatement simulation

change option char of wanted_size from "S" to "l" (for wanted sequence length) to avoid similar option char with seed option