Overhaul (#435)

* Introduces new data models

* Overhaul old code

* Refinements

* Renames modules to 'topsoil-'

* Adds data parser tests

* Change home screen to allow recent file list

* Adds unit testing for file parsing and serialization

* Implements most former MenuItem behavior

* TreeTable fixes, further test revisions

* Fixes ProjectTreeView and ConstantsEditor in project view

* Changes package structure to be more logical

* Renames some classes with 'Topsoil-' in the name

* Adds parameterized type to DataColumn; models implement Serializable

* Shows data values in TreeTableView

* Adds documentation

* Shows correct values in table

* Refactors DataParsers

* Recreates new project wizard

* Fixes bugs in file parsing

* Fixes bugs in serialization

* Improves exception handling for controls and serializer

* Implements default table export

* Fixes import from clipboard

* Adds getDepth method for DataComposites

* Fixes bug in Squid3DataParser

* Closes ProjectView if last tab closed

* Adds more javadoc

* Enables CheckBoxes in main TreeTableView

* Fixes plotting for sample data

* Enables column selection

* Adds lines between data rows

* Fixes ellipse selection

* Fixes variable chooser

* Makes row selection live in plot

* Adds notification when trying to export non-default table

* Moves file package up from util

* Removes table in ProjectTreeView when table tab closed

* Implements recent files

* Fixes ConcurrentModificationException in ProjectTreeView

* Aligns data values by decimal separator

* Fixes serialization bugs

* Fixes ProjectView resizing bug

* Combines table options view and variable chooser

* Keeps DataTable list consistent within a project

* Renames application class to 'Topsoil'

* Splits DataTable into that and DataRoot

* Implements TableObserver for updating plots

* Removes converter attribute from DataColumn

* Creates single serializable class

* Removes StyleLoader

* Renames 'samples' to 'examples'

* Gets rid of 'Title' section of New Project Wizard

* Addresses variable chooser sizing

* Moves multiple import functionality to import menu

* Parsers mark duplicate columns

* Fixes variable chooser selection when columns are hidden

* Pre-selects 204-corr columns for squid3 data

* Adds 'Classic' data template to select the first five data columns

* Aligns 'Project Structure' and 'Constants Editor' labels

* Fixes current lambda values

* Adds ASCII logo

* Implements clear recent files

* Cleans up utility code and menu items

* Centers initial view

* Fixes row labels in project structure panel

* Fixes default table sorting

* Removes data features from plot when deselected

* Uses correct Base64 class in PDFSaver

* Adds main class to jarWithDependencies

* Centers initial stage on screen before showing

* Moves hard-coded strings to resource bundles

* Adds basic tests for data classes

* Loads custom font properly

* Prevents mouse-wheel scrolling on variable chooser

* Project column selections are read back in correctly

* Fixes bug in McLean Regression

* Removes extra Edit menu item

* Corrects concordia selection behavior

* Fixes javadoc errors

* Saved pdf files are scalable

* Cleans up ProjectView code

* Moves all resource bundles to one place

* Refactors DataRow

* Turns off autodetect fonts on PDFTranscoder

* Variable assignments stored in topsoil file

* Passes failing test

* Hides scrollbars on VariableChooser

* Displays message if no tables are loaded

* Removes files from recent list if nonexistent

* Recent files show full path

* Adjusts variable chooser size if many columns

* Fixes column visibility bug in DataTableOptionsView

* Fixes bottom border of variable chooser

* Moves current project and project path to ProjectManager

* Adds more javadoc; removes unnecessary code

* Prevents duplicate plots, instead requests focus of open plot

* Project files restore open plots and lambda settings

* Removes getController() in Topsoil

* Separates TopsoilPlotView and TopsoilProject

* Condenses concordia controls

* Checks that required variables are assigned

* Plots can be resized without a boundary

* Cleans up SerializableProject

* Solves bug in VariableChooser

* Limits fraction digits for axes extents live update