This moves the script to the vendored directory, which is a git subtree
of https://github.com/nextstrain/ingest (currently at branch
apply-geolocation-rules). The file suffix is removed to match how it
appears in the other repos which use it.

As per [Overview of duplicated scripts](#1)
this script also appears in:
* [monkeypox](https://github.com/nextstrain/monkeypox/blob/a1f0d7b757d323d87edcbe61c6c5ccfbdf47722c/ingest/bin/apply-geolocation-rules)
* [rsv](https://github.com/nextstrain/rsv/blob/ba171f4a43110382c38b6154be3febd50408d7bf/ingest/bin/apply-geolocation-rules)
* [dengue, branch new_ingest](https://github.com/nextstrain/dengue/blob/247b2fd897361f2548627de1d97d45fae4115c5c/ingest/bin/apply-geolocation-rules)

All three of those scripts are identical to each other. The script vendored
here contains two code changes (whitespace removed from diffs):

**Ignore comment lines in the location-rules TSV**
```diff
< if line.lstrip()[0] == '#':
---
> if line.strip()=="" or line.lstrip()[0] == '#':
```

**Allow fields to be missing from the input NDJSON**

The script previously mandated that the input NDJSON had all four
fields (region/country/division/location). This is relaxed here, with
an empty string used if the field is not present.

```diff
< annotated_values = transform_geolocations(geolocation_rules, [record[field] for field in location_fields])
---
> annotated_values = transform_geolocations(geolocation_rules, [record.get(field, '') for field in location_fields])
```