Upgraded NPM packages with npm upgrade

[gaurav]

This won't fix all the dependabot issues, but it should help. To fully fix all those issues, we'll need to replace all the packages with their latest versions, starting with our own @phyloref/phyx, which is very out of date.

$ npm outdated
Package                    Current  Wanted  Latest  Location                                Depended by
@phyloref/phyx               0.2.1   0.2.1   1.2.1  node_modules/@phyloref/phyx             clade-ontology
ajv                         6.12.6  6.12.6  8.17.1  node_modules/ajv                        clade-ontology
chai                         4.5.0   4.5.0   6.2.1  node_modules/chai                       clade-ontology
eslint                      5.16.0  5.16.0  9.39.1  node_modules/eslint                     clade-ontology
eslint-config-airbnb-base   13.2.0  13.2.0  15.0.0  node_modules/eslint-config-airbnb-base  clade-ontology
eslint-plugin-json           1.4.0   1.4.0   4.0.1  node_modules/eslint-plugin-json         clade-ontology
eslint-plugin-mocha          5.3.0   5.3.0  11.2.0  node_modules/eslint-plugin-mocha        clade-ontology
mocha                        5.2.0   5.2.0  11.7.5  node_modules/mocha                      clade-ontology
tmp                          0.1.0   0.1.0   0.2.5  node_modules/tmp                        clade-ontology
yargs                       13.3.2  13.3.2  18.0.0  node_modules/yargs                      clade-ontology