How peers are resolved
One of the best features of pnpm is that in one project, a specific version of a package will always have one set of dependencies. There is one exception from this rule, though - packages with peer dependencies.
Peer dependencies are resolved from dependencies installed higher in the dependency graph, since they share the same version as their parent. That means that if foo@1.0.0 has two peers (bar@^1 and baz@^1) then it might have multiple different sets of dependencies in the same project.
- foo-parent-1
  - bar@1.0.0
  - baz@1.0.0
  - foo@1.0.0
- foo-parent-2
  - bar@1.0.0
  - baz@1.1.0
  - foo@1.0.0
In the example above, foo@1.0.0 is installed for foo-parent-1 and foo-parent-2. Both packages have bar and baz as well, but they depend on different versions of baz. As a result, foo@1.0.0 has two different sets of dependencies: one with baz@1.0.0 and the other one with baz@1.1.0. To support these use cases, pnpm has to hard link foo@1.0.0 as many times as there are different dependency sets.
Normally, if a package does not have peer dependencies, it is hard linked to a node_modules folder next to symlinks of its dependencies, like so:
node_modules
└── .pnpm
    ├── foo@1.0.0
    │   └── node_modules
    │       ├── foo
    │       ├── qux   -> ../../qux@1.0.0/node_modules/qux
    │       └── plugh -> ../../plugh@1.0.0/node_modules/plugh
    ├── qux@1.0.0
    ├── plugh@1.0.0
However, if foo has peer dependencies, there may be multiple sets of dependencies for it, so we create different sets for different peer dependency resolutions:
node_modules
└── .pnpm
    ├── foo@1.0.0_bar@1.0.0+baz@1.0.0
    │   └── node_modules
    │       ├── foo
    │       ├── bar   -> ../../bar@1.0.0/node_modules/bar
    │       ├── baz   -> ../../baz@1.0.0/node_modules/baz
    │       ├── qux   -> ../../qux@1.0.0/node_modules/qux
    │       └── plugh -> ../../plugh@1.0.0/node_modules/plugh
    ├── foo@1.0.0_bar@1.0.0+baz@1.1.0
    │   └── node_modules
    │       ├── foo
    │       ├── bar   -> ../../bar@1.0.0/node_modules/bar
    │       ├── baz   -> ../../baz@1.1.0/node_modules/baz
    │       ├── qux   -> ../../qux@1.0.0/node_modules/qux
    │       └── plugh -> ../../plugh@1.0.0/node_modules/plugh
    ├── bar@1.0.0
    ├── baz@1.0.0
    ├── baz@1.1.0
    ├── qux@1.0.0
    ├── plugh@1.0.0