fix: Drop coverage produced by nyc --all for files that were tested

Sometimes the coverage data produced by `nyc --all` is incompatible with
the coverage data produced by actual test runs.  This is generally due
to configuration error but results in inconsistent coverage reports or
in some cases causes `nyc report` to crash.  The workaround is
implemented in istanbul-lib-coverage to drop coverage data associated
with `nyc --all` when coverage data from a test run is found.  This
commit tags the coverage data when appropriate so the coverage merge
logic knows what to do.

Fixes istanbuljs#1113, istanbuljs#1124, istanbuljs#1148

index.js

@@ -170,7 +170,11 @@ class NYC {
       const coverage = coverageFinder()
       const lastCoverage = this.instrumenter().lastFileCoverage()
       if (lastCoverage) {
-        coverage[lastCoverage.path] = lastCoverage
+        coverage[lastCoverage.path] = {
+          ...lastCoverage,
+          // Only use this data if we don't have it without `all: true`
+          all: true
+        }
       }
     })
     this.fakeRequire = false