fix(core): deleted projects should not be in cached graph

[AgentEnder]

Current Behavior

After refactoring JS into its own subfolder, projects that had been deleted are still present in the project graph and this causes some serious issues after deleting a project. (ref: #15365)

Expected Behavior

Deleting a project causes the graph builder to recompute from scratch.

Related Issue(s)

Fixes #16091
Fixes nrwl/nx-console#1659

[vercel]

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Name	Status	Preview	Comments	Updated (UTC)
nx-dev	✅ Ready (Inspect)	Visit Preview	💬 Add feedback	Apr 10, 2023 10:37pm

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✅ Successfully ran 8 targets

• nx affected -t e2e-macos --parallel=1 --exclude=e2e-detox
• nx affected --target=e2e --base=149ad5ab17f5c6c7b5b27d044b787280ffb34847 --head=f8ef99a6d72c48537b8ca97b962692ff264b637a --parallel=1
• nx affected --target=test --base=149ad5ab17f5c6c7b5b27d044b787280ffb34847 --head=f8ef99a6d72c48537b8ca97b962692ff264b637a --parallel=1
• nx affected --target=build --base=149ad5ab17f5c6c7b5b27d044b787280ffb34847 --head=f8ef99a6d72c48537b8ca97b962692ff264b637a --parallel=3
• nx run-many -t check-imports check-commit check-lock-files depcheck --parallel=1 --no-dte
• nx affected --target=lint --base=149ad5ab17f5c6c7b5b27d044b787280ffb34847 --head=f8ef99a6d72c48537b8ca97b962692ff264b637a --parallel=3
• nx-cloud record -- nx format:check --base=149ad5ab17f5c6c7b5b27d044b787280ffb34847 --head=f8ef99a6d72c48537b8ca97b962692ff264b637a
• nx documentation --no-dte

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