- create developer's guide
  - start using `#!` for comments to stay
  - this is only info in guide for now
- broader use of `haskey`
- `InputFolder` class now includes: `location`, `basename`, `required`, `varied`, and `path_from_inputs`
  - Inner constructors help initialize from just `location` + (`id` OR `folder` OR both)
- `InputFolders` now a wrapper for a `NamedTuple` where the keys are locations (stored in `project_locations.all`) and the values are of type `InputFolder`
  - users are expected to use either the keyword arg constructor (`InputFolders(; kwargs...)`) or the parse-time defined `InputFolders(<required_locations...>; <optional_locations...>)` where the `inputs.toml` determines the parameter/keyword arg names
  - users could create a vector of pairs, but this is expected to be used internally
  - `getindex` is implemented to allow for `input_folders[:config]` to access the values of the `NamedTuple`
- `VariationID` replaces `VariationIDs` and is now just a wrapper for a `NamedTuple`
  - handles construction of default variation ids based on the folder ID being -1 or not
  - `getindex` implemented to allow for `variation_id[:config]` to access the id for the config variation
- better checks on instantiating `Simulation`s
- make use of `project_locations` in just so many helpful ways
- functions to simplify adding output types to vct.db
- one function each for setting table names (`"$(loc)s"`), loc ids (`"$(loc)_id"`) and loc var ids (`"$(loc)_variation_id"`)
- support for roadrunner sims!
  - will download roadrunner if needed and then go ahead and run the sims
  - checks for environment variables needed, sets in the julia runtime if need be, and helps the user to fix this
  - printls helpful message if not present
- `locationPath` to standardize how to access `inputs`
- starting to support components that containt, well, components of simulation inputs
  - these will live in `data/components` and can be used outside of `run` to set up different input/location folders
  - added `VCTComponents.jl` (though it could be renamed to `VCTIntracellularComponents.jl`) to manage combining of components together
- standardize loading of input folders using `createXMLFile`
- `inputs.toml` now allows users to decide on the structure of their project at runtime
- rewrite of VCTDatabase using inputs.toml
- `initializeVCT` replaced by `initializeModelManager` and can accept no arguments to initialize from the current directory
- `make clean` only in the `temp_physicell_dir`
- compilation `cmd` gets the `ENV` passed in (so the librr var can be included) and also the `temp_physicell_dir` to make sure everything is in that location
- print entire compile `cmd` rather than just the `cflags` (though first get rid of the env and dir info because those make it hard to read)
- on compilation failure, print the log and err to console
- `prepareInputFolder` function now gives a generic interface for initializing each input
- `cmd` for running the sim now has `env` and `dir` set to ensure necessary flags are passed in and that it is being run from teh PHysiCell directory
- `--chdir=$(physicell_dir)` now set for `sbatch` command to make sure it is being run from that directory. still need to see if the env is being properly set there or if that requires extra attention
- bundle results of `addVariations` into an `AddVariationsResult` type so those only output one thing
- `sqliteDataType(ev::ElementaryVariation)` to standardize how all database types are determined
- VCTComponents doc