fix: don't shift output when a dependency resolves to a .ts file

[dsherret]

When a dependency's resolution lands on a .ts file, TypeScript pulls it into the program as a source file rather than a declaration file. That moved the inferred common source directory from <outDir>/src up to <outDir>, so every emitted file gained an extra src segment while the package.json paths — built from the transform's entry point paths — did not:

npm/esm/node_modules/type-detect/index.js   <-- a dependency got compiled
npm/esm/src/mod.js                          <-- extra "src" segment
npm/types/mod.d.ts                          <-- no "src" segment

{ "module": "./esm/mod.js" }                 // points at nothing

Pinning rootDir to the sources keeps the output where the package.json says it is, and stops the dependency being emitted into the package.

Type checking hit the same file for the second half of the problem — skipLibCheck only covers a dependency's .d.ts files, so a dependency shipping .ts reported its own errors against the package author (14 of them for type-detect, ex. Cannot find name 'window'). Its code is no more the author's problem than a .d.ts would be, so diagnostics from node_modules are ignored the same way.

The regression test uses type-detect@^4.1.0, which has no types/typings entry and ships index.js, index.d.ts and index.ts. Nothing is specific to that package — any dependency shipping a .ts file that resolution lands on does it. The test fails on both counts without the fix.

Closes #460