Runfiles tree is not recreated when value of `--enable_runfiles` changes

Or more precisely, the old tree persists even when the target is built with `--enable_runfiles=false`. This causes observable semantic differences when the artifact is sensitive to how the runfiles tree is laid out (or whether it exists at all).

Minimal repro:

```python
# pkg/BUILD
cc_binary(
name = "blah",
srcs = ["blah.cc"],
)
```

```cc
// pkg/blah.cc
#include

int main(int argc, char** argv) {
printf("Hello, world!\n");
return 0;
}
```

```sh
$ bazel clean
...
$ bazel run //pkg:blah
...
$ ls bazel-bin/pkg/blah.runfiles
__main__ MANIFEST

$ bazel run //pkg:blah --enable_runfiles=false
...
$ ls bazel-bin/pkg/blah.runfiles
__main__ MANIFEST

$ bazel clean
...
$ bazel run //pkg:blah --enable_runfiles=false
...
$ ls bazel-bin/pkg/blah.runfiles
MANIFEST
```

Reproduce the issue with the two `bazel run //pkg:blah` commands shown, both before and after `bazel clean`, and inspect `bazel-bin/pkg/blah.runfiles`. Start by tracing the runfiles tree creation and invalidation for `--enable_runfiles`; done means changing the flag removes or recreates the tree so stale `__main__` contents do not persist.

Written by the indexing model from the issue text.