- Fix the runtime missing certain files
- Fix local runtime file serving logic

These changes make it possible to run a `pull`-ed site using the local
sqlite runtime, e.g.:
```
php importer/import.php pull https://mymigrationwpcloudsite.wpcomstaging.com/ \
  --secret=SECRET_GOES_HERE\
  --state-dir=./exports/state --fs-root=./exports/files \
  --new-site-url=http://localhost:8881
```