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Store layout

pnpm maintains a flat storage of all your dependencies in node_modules/.store. They are then symlinked whereever they're needed. This is like npm@2's recursive module handling (without the disk space bloat), and like npm@3s flat dependency tree (except with each module being predictably atomic). To illustrate, an installation of chalk@1.1.1 may look like this:

.
└─ node_modules/
   ├─ .store/
   │  ├─ chalk@1.1.1/_/
   │  │  └─ node_modules/
   │  │     ├─ ansi-styles      -> ../../../ansi-styles@2.1.0/_
   │  │     ├─ has-ansi         -> ../../../has-ansi@2.0.0/_
   │  │     └─ supports-color   -> ../../../supports-color@2.0.0/_
   │  ├─ ansi-styles@2.1.0/_/
   │  ├─ has-ansi@2.0.0/_/
   │  └─ supports-color@2.0.0/_/
   └─ chalk                     -> .store/chalk@1.1.1/_

The intermediate _ directories are needed to hide node_modules from npm utilities like npm ls, npm prune, npm shrinkwrap and so on. The name _ is chosen because it helps make stack traces readable.

Peer dependencies

Symlinks to deep dependencies are stored in node_modules/.store/node_modules, in addition to the diagram above. It looks something like this:

.
└─ node_modules/
   ├─ .store/
   │  ├─ chalk@1.1.1/_/
   │  ├─ ansi-styles@2.1.0/_/
   │  ├─ has-ansi@2.0.0/_/
   │  └─ node_modules/
   │     └─ ansi-styles         -> ../ansi-styles@2.1.0/_
   │     └─ has-ansi            -> ../has-ansi@2.0.0/_
   └─ chalk                     -> .store/chalk@1.1.1/_

In the example above, this allows ansi-styles to require('has-ansi'). This is necessary to make certain packages work, such as standard (eslint + eslint-config-standard).