Deprecate `in-source` flag

[cometkim]

See #6209 (comment)

Currently in-source is optional, and the compiler only does one mode.

However, they have their own use cases and are not interchangeable. In particular, with ESM semantics, a lib directory is still needed to serve without additional tools like NPM.

However, most people use in-source: true in the general case as we recommended it.

I think that both should be enabled. Users only have to choose whether to include it in the NPM package or the git repository.

[cometkim]

Related #6210 and #6475