Fix adding packages in workspaces

[Jarred-Sumner]

What does this PR do?

Fixes bugs involving:

• adding dependencies to workspaces
• editing workspace package.json
• diffing lockfiles with workspace dependencies

fixes #11064
fixes #9413
fixes #7913
fixes #7844
fixes #7547

Also adds a better error message when the directory given to --cwd doesn't exist.

How did you verify your code works?

added tests

[github-actions]

❌ @dylan-conway, your commit has failing tests :(

💪 3 failing tests Darwin AARCH64

• test/cli/install/registry/bun-install-registry.test.ts 5 failing
• test/js/bun/http/serve.test.ts 2 failing
• test/js/node/http2/node-http2.test.js 1 failing

💻 3 failing tests Darwin x64 baseline

• test/js/bun/http/serve.test.ts 2 failing
• test/js/node/dns/node-dns.test.js 1 failing
• test/js/web/workers/worker.test.ts 1 failing

💻 2 failing tests Darwin x64

• test/js/bun/http/serve.test.ts 2 failing
• test/js/bun/test/test-test.test.ts 1 failing

🐧🖥 1 failing tests Linux x64 baseline

• test/js/node/child_process/child_process-node.test.js 1 failing

🐧🖥 1 failing tests Linux x64

• test/js/node/child_process/child_process-node.test.js 1 failing

🪟💻 9 failing tests Windows x64 baseline

• test/cli/install/bunx.test.ts 1 failing
• test/integration/esbuild/esbuild.test.ts 1 failing
• test/integration/next-pages/test/dev-server.test.ts 1 failing
• test/js/bun/shell/bunshell.test.ts 1 failing
• test/js/bun/shell/commands/rm.test.ts 1 failing
• test/js/node/dns/node-dns.test.js 2 failing
• test/js/node/process/process.test.js 2 failing
• test/js/node/watch/fs.watchFile.test.ts 3 failing
• test/js/web/workers/worker.test.ts 2 failing

🪟💻 10 failing tests Windows x64

• test/bundler/large_asset_regression.test.ts 1 failing
• test/cli/install/bunx.test.ts 1 failing
• test/cli/install/registry/bun-install-registry.test.ts SIGTERM
• test/integration/esbuild/esbuild.test.ts 1 failing
• test/integration/next-pages/test/dev-server.test.ts 1 failing
• test/js/bun/shell/bunshell.test.ts 1 failing
• test/js/node/dns/node-dns.test.js 2 failing
• test/js/node/process/process.test.js 2 failing
• test/js/node/watch/fs.watchFile.test.ts SIGTERM
• test/js/web/workers/worker.test.ts 2 failing

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