allowed-fixmes.jq

[
  .errors[].message[]
  | select(.descr | startswith("You cannot use HH_FIXME"))
  | (
    if .path | endswith(".hackpartial")
    then  { it: ., option: "allowed_fixme_codes_partial" }
    else  { it: ., option: "allowed_fixme_codes_strict" }
    end
  )
  | (
    if .it.descr | endswith("in declarations")
    then
      [
        { code: .it.code, option: .option },
        { code: .it.code, option: "allowed_decl_fixme_codes" }
      ]
    else [ { code: .it.code, option: .option } ]
    end
  )
]
| flatten
| group_by(.option)
| .[]
| {
  option: .[0].option,
  codes: map(.code) | unique | sort
}
|.option+"="+(.codes|join(","))

Usage

hh_server --check . --json | jq -r "$(<allowed-fixmes.jq)" >> .hhconfig