Fix custom reference_data support in as.sir() (fixes #239)

- custom guideline names now correctly classify values as R: CLSI convention
  (>= breakpoint_R for MIC, <= for disk) applies only when guideline contains
  "CLSI"; all other guidelines including custom ones use the EUCAST convention
  (> breakpoint_R for MIC, < for disk)
- guideline argument is now optional when reference_data is manually set: if
  omitted or if its value does not match any row in the custom data, all rows
  in reference_data are used; if set to a value present in the data, only
  matching rows are filtered — useful for multi-guideline custom tables
- host = NA in custom reference_data now acts as a host-agnostic fallback
  when no host-specific breakpoint row exists for the current animal species
- updated reference_data argument documentation to explain these conventions

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

NEWS.md

@@ -21,6 +21,7 @@
 * Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
 
 ### Fixes
+* `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (fixes #239)
 * Fixed multiple bugs in the `parallel = TRUE` mode of `as.sir()` for data frames: (1) PSOCK workers (Windows / R < 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of `AMR_env` instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (`mclapply`) where pre-existing `sir_interpretation_history` rows were included in every worker's captured log; (4) removed use of non-exported internal functions (`%pm>%`, `pm_pull`, `as.sir.default`) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape `\u00a` (3 digits) in the "DONE" status message
 * Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
 * Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved