Ichthyop

Bug fix

- Resolve a problem in the saving of XML Zone files on Windows. Encoding was automatically set to Cp1512, not handled by XML. Now UTF-8 should be saved. Bug was corrected for configuration files in 3.3.6 but not for zone files.

Bug fix

- Add the `units` attribute (which replaces the `origin` attribute) to the time variable. It was lost with the new time management in Ichthyop.
- **Correct bug in template creation (templates were considered as resources by Ichthyop but were kept in `java` folder, which was not used as resource folder).**

New features

- Resources have been moved in a new folder (`src/main/resources`). This allows the VSCOde debugger to work more nicely (debugging in `java` files and not in `class` files).

Bug fix

- Template configuration and forcing files have been updated to match the new management of time (use of units attributes in the NetCDF)
- Closing of NetcdfFile in the `getDate()` method (`DatasetUtil.java`), which causes errors after multiple opening (pointed out by Amael Dupaix)

Bug fix

- Correct output issue when running multiple simulations (pointed out by Amael Dupaix)

New features

- Remove all warnings (VSCode)
- Remove deprecated NetCDF functions, use new NetCDF implementation
- Re-add the `WaveDriftFileAction.java` file.
- New constructor for the `InterAnnualCalendar` object
- Saving the stage values in the `DebGrowthAction.java`

Bug fix

- Correction of the pC calculation in the classical DEB (forgot Tahr correction) + change starvation correction (`||` instead of `&&`)
- Correction in the saving of zones areas: `zoneX` is the dimension (number of points) while `coord_zoneX` is the coordinates of each point. Allows to read file using Python Xarray without problems.
- Correction in the time management in Ichthtyop. Use `LocalDateTime` extensively.
- Correction in the lock of particles when recruited. This insures that analysing recruitment from `zones` or `recruited_zones` variables gives the same result (spotted by Stephane Pous)
- Correction of a bug in the saving of ouput file with Zones + Gui (spotted by Stephane Pous)
- Correction of a bug in the display of zones in GUI (used the wrong variable to display variables on maps)
- Do not include a user-defined track variable if already included (for instance `temperature` in `LethalTempAction.java`)

Bug fixes

- Resolve a problem in the saving of XML configuration files on Windows. Encoding was automatically set to Cp1512, not handled by XML. Now UTF-8 should be saved.