Lots of warnings when installing

When I do a fresh install, I see tons of install warnings (due to deprecated packages):

$ rm -rf node_modules/
$ npm install

npm WARN deprecated babel-preset-es2015@6.24.1: 🙌  Thanks for using Babel: we recommend using babel-preset-env now: please read babeljs.io/env to update!
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 to-iso-string@0.0.2: to-iso-string has been deprecated, use @segment/to-iso-string instead.
npm WARN deprecated minimatch@0.3.0: 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.

> execSync@1.0.2 install [path redacted]/shx/node_modules/execSync
> node install.js

[execsync v1.0.2] Attempting to compile native extensions.
[execSync v1.0.2]
    Native code compile failed!!
npm WARN prepublish-on-install As of npm@5, `prepublish` scripts are deprecated.
npm WARN prepublish-on-install Use `prepare` for build steps and `prepublishOnly` for upload-only.
npm WARN prepublish-on-install See the deprecation note in `npm help scripts` for more information.

> shx@0.3.0 prepublish [path redacted]/shx
> npm run build


> shx@0.3.0 prebuild [path redacted]/shx
> rimraf lib


> shx@0.3.0 build [path redacted]/shx
> babel src -d lib

src/cli.js -> lib/cli.js
src/config.js -> lib/config.js
src/help.js -> lib/help.js
src/printCmdRet.js -> lib/printCmdRet.js
src/shx.js -> lib/shx.js
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.4 (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.4: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

added 690 packages in 22.104s

Of these issues, graceful-fs is probably the most pressing (updating codecov resolves this).