With the latest update the extension now works on header files out of the box. More details on the project page.
From the changelog:
## [0.0.4]
- Speed up diagnostics by limiting how often iwyu is run and apply heuristics to early skip source scanning.
- Add new config settings:
- `iwyu.diagnostics.iwyu_interval`: Minimum interval time in seconds between iwyu calls.
- `iwyu.diagnostics.only_re`: Only compute diagnostics for files that match this regexp.
- `iwyu.diagnostics.scan_min`: Scan at least this many lines, if no include is found, then stop.
- `iwyu.diagnostics.scan_more`: After finding an include, scan at least this many more lines.
# [0.0.5]
- Per file IWYU data handling.
- Improved header processing:
- Rename `iwyu.fix.safe` to `iwyu.fix.safe_headers` to match the actual argument name.
- Change `iwyu.fix.safe_headers` to default to false, so that the tool works for headers by default.
- Provide `--basedir` to `fix_includes.py` invocation to explicitly apply fixes only to the selected file.
- Change `iwyu.fix.comments` to default to false.
- Add `iwyu.fix.dry_run` config for additional debugging.
- Add `iwyu.fix.update_comments` to go along with `iwyu.fix.comments`.