Address deprecation warnings during npm install

[wooldridge]

Currently, deprecation warnings about outdated dependencies appear during npm install:

npm WARN deprecated gulp-jsdoc@0.1.5: This project is deprecated. Use gulp-jsdoc3 instead.
npm WARN deprecated minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated minimatch@0.2.14: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated graceful-fs@1.2.3: graceful-fs v3.0.0 and before will fail on node releases >= v7.0. Please update to graceful-fs@^4.0.0 as soon as possible. Use 'npm ls graceful-fs' to find it in the tree.
npm WARN deprecated wrench@1.5.9: wrench.js is deprecated! You should check out fs-extra (https://github.com/jprichardson/node-fs-extra) for any operations you were using wrench for. Thanks for all the usage over the years.
npm WARN deprecated wrench@1.3.9: wrench.js is deprecated! You should check out fs-extra (https://github.com/jprichardson/node-fs-extra) for any operations you were using wrench for. Thanks for all the usage over the years.
npm WARN deprecated to-iso-string@0.0.2: to-iso-string has been deprecated, use @segment/to-iso-string instead.
npm WARN deprecated jade@0.26.3: Jade has been renamed to pug, please install the latest version of pug instead of jade
npm WARN deprecated minimatch@0.3.0: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN prefer global marked@0.3.6 should be installed with -g

Some of these warnings will go away after we update our jsdoc and gulp-jsdoc libraries, see #363. After that is taken care of, we can look at the remaining warnings and see what can be addressed.

This issue came out of #343.

[wooldridge]

After having updated the jsdoc and gulp-jsdoc3 libraries in #363, we have fewer deprecation complaints during npm install. As of 14ba294:

npm WARN deprecated minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated minimatch@0.2.14: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated graceful-fs@1.2.3: graceful-fs v3.0.0 and before will fail on node releases >= v7.0. Please update to graceful-fs@^4.0.0 as soon as possible. Use 'npm ls graceful-fs' to find it in the tree.
npm WARN prefer global marked@0.3.6 should be installed with -g

The above deprecation warnings are due to subdependencies of other libraries that we can't do anything about:

minimatch@2.0.10 - subdependency of glob-stream@3.1.18, under gulp 3.9.1
minimatch@0.2.14 - subdependency of globule@0.1.0, under gulp 3.9.1
graceful-fs@1.2.3 - subdependency of glob@3.1.21, under gulp 3.9.1
marked@0.3.6 - subdependency of jsdoc@3.4.3

Closing this issue.