How do you compile files with multiple dependencies (imports and .jar files)?

I have the following directory structure:

I'm having trouble compiling the source files in the 'models' package, which rely on all other files in packages src as well as the .jar file in lib. How would I write the classpath command to compile these model files (on mac)?

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joseph@Josephs-MacBook-Pro models % javac -cp ".:.." NeuralNetworkMultiClass.java
../utils/Metrics.java:4: error: package org.knowm.xchart.style does not exist
import org.knowm.xchart.style.AxesChartStyler;
                             ^
../utils/Metrics.java:5: error: package org.knowm.xchart.style does not exist
import org.knowm.xchart.style.Styler;
                             ^
../utils/Metrics.java:6: error: package org.knowm.xchart.style.markers does not exist
import org.knowm.xchart.style.markers.SeriesMarkers;
                                     ^
../utils/Metrics.java:3: error: package org.knowm.xchart does not exist
import org.knowm.xchart.*;
^
../utils/Metrics.java:34: error: cannot find symbol
        XYChart chart = new XYChartBuilder()
        ^
  symbol:   class XYChart
  location: class Metrics
../utils/Metrics.java:34: error: cannot find symbol
        XYChart chart = new XYChartBuilder()
                            ^
  symbol:   class XYChartBuilder
  location: class Metrics
../utils/Metrics.java:50: error: cannot find symbol
        XYSeries series = chart.addSeries(seriesName, xData, yData);
        ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:51: error: cannot find symbol
        series.setMarker(SeriesMarkers.NONE);
                         ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:52: error: cannot find symbol
        new SwingWrapper<>(chart).displayChart();
            ^
  symbol:   class SwingWrapper
  location: class Metrics
../utils/Metrics.java:69: error: cannot find symbol
        ArrayList<XYChart> charts = new ArrayList<>();
                  ^
  symbol:   class XYChart
  location: class Metrics
../utils/Metrics.java:74: error: cannot find symbol
        XYChart chart = new XYChartBuilder()
        ^
  symbol:   class XYChart
  location: class Metrics
../utils/Metrics.java:74: error: cannot find symbol
        XYChart chart = new XYChartBuilder()
                            ^
  symbol:   class XYChartBuilder
  location: class Metrics
../utils/Metrics.java:81: error: cannot find symbol
        XYSeries costA1 = chart.addSeries("Alpha = 1", xData, ySeries[0]);
        ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:82: error: cannot find symbol
        XYSeries costA2 = chart.addSeries("Alpha = 0.1" , xData, ySeries[1]);
        ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:83: error: cannot find symbol
        XYSeries costA3 = chart.addSeries("Alpha = 0.01", xData, ySeries[2]);
        ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:84: error: cannot find symbol
        costA1.setMarker(SeriesMarkers.NONE);
                         ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:85: error: cannot find symbol
        costA2.setMarker(SeriesMarkers.NONE);
                         ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:86: error: cannot find symbol
        costA3.setMarker(SeriesMarkers.NONE);
                         ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:90: error: cannot find symbol
        new SwingWrapper<>(charts).displayChartMatrix();
            ^
  symbol:   class SwingWrapper
  location: class Metrics
../utils/Metrics.java:108: error: cannot find symbol
        ArrayList<XYChart> charts = new ArrayList<>();
                  ^
  symbol:   class XYChart
  location: class Metrics
../utils/Metrics.java:116: error: cannot find symbol
            XYChart chart = new XYChartBuilder()
            ^
  symbol:   class XYChart
  location: class Metrics
../utils/Metrics.java:116: error: cannot find symbol
            XYChart chart = new XYChartBuilder()
                                ^
  symbol:   class XYChartBuilder
  location: class Metrics
../utils/Metrics.java:123: error: cannot find symbol
            XYSeries cost = chart.addSeries("training", xData, ySeries[i]);
            ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:124: error: cannot find symbol
            XYSeries recall = chart.addSeries("validation", xData, ySeries[i + 1]);
            ^
  symbol:   class XYSeries
  location: class Metrics
../utils/Metrics.java:125: error: cannot find symbol
            cost.setMarker(SeriesMarkers.NONE);
                           ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:126: error: cannot find symbol
            recall.setMarker(SeriesMarkers.NONE);
                             ^
  symbol:   variable SeriesMarkers
  location: class Metrics
../utils/Metrics.java:131: error: cannot find symbol
        new SwingWrapper<>(charts).displayChartMatrix();
            ^
  symbol:   class SwingWrapper
  location: class Metrics
27 errors

You're running the command from projectDir/src/models but NeuralNetworkMultiClass.java depends on other packages as well.

You could run the java compiler from projectDir and place all compiled class files inside out:

javac -cp "src:lib/*" -d out src/*/*.java

Then if you, for example, want to run NeuralNetworkMultiClass, you do it from projectDir like so:

java -cp "out:lib/*" models.NeuralNetworkMultiClass

Refer to this and this on platform specifics when specifying a list of files/folders to the -cp flag.