fix: pnpm prune misses root dependency (vercel#3483)

Fixes vercel#2798 which comprised of two issues:
- We eagerly checked if a version specifier was already resolved in the
package list. This can lead to grabbing a version of the package that
doesn't have the expected peer dependencies. This was as easy as moving
this check after we have gone down the happy path.
- Not copying internal dependencies of the monorepo root. We now
internally add `//` to the prune scope to make sure we get any internal
dependencies.

For reviewers: I highly recommend reviewing the first commit in this PR
initially as it unifies the pnpm lockfile implementations. I realized
that my code split was unnecessary and made fixing bugs for lockfile v5
and v6 very difficult.

cli/integration_tests/prune/includes_root_deps.t

@@ -0,0 +1,10 @@
+Setup
+  $ . ${TESTDIR}/../setup.sh
+  $ . ${TESTDIR}/setup.sh $(pwd)
+
+Make sure that the internal util package is part of the prune output
+  $ ${TURBO} prune --scope=web
+  Generating pruned monorepo for web in .*/out (re)
+   - Added shared
+   - Added util
+   - Added web

cli/integration_tests/prune/monorepo_with_root_dep/apps/docs/package.json

@@ -0,0 +1,6 @@
+{
+  "name": "docs",
+  "dependencies": {
+    "shared": "workspace:*"
+  }
+}

cli/integration_tests/prune/monorepo_with_root_dep/apps/web/package.json

@@ -0,0 +1,6 @@
+{
+  "name": "web",
+  "dependencies": {
+    "shared": "workspace:*"
+  }
+}

cli/integration_tests/prune/monorepo_with_root_dep/package.json

@@ -0,0 +1,7 @@
+{
+  "name": "monorepo",
+  "packageManager": "[email protected]",
+  "devDependencies": {
+    "util": "workspace:*"
+  }
+}

cli/integration_tests/prune/monorepo_with_root_dep/packages/shared/package.json

@@ -0,0 +1,3 @@
+{
+  "name": "shared"
+}

cli/integration_tests/prune/monorepo_with_root_dep/packages/util/package.json

@@ -0,0 +1,3 @@
+{
+  "name": "util"
+}

cli/integration_tests/prune/monorepo_with_root_dep/pnpm-workspace.yaml

@@ -0,0 +1,3 @@
+packages:
+  - "apps/*"
+  - "packages/*"

cli/integration_tests/prune/monorepo_with_root_dep/turbo.json

@@ -0,0 +1,4 @@
+{
+  "$schema": "https://turbo.build/schema.json",
+  "pipeline": {}
+}

cli/integration_tests/prune/setup.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+SCRIPT_DIR=$(dirname ${BASH_SOURCE[0]})
+TARGET_DIR=$1
+cp -a ${SCRIPT_DIR}/monorepo_with_root_dep/. ${TARGET_DIR}/