Add {.topic} markup for non-function help page references

Replace {.code ?AMR-options} and backtick-style ?AMR-options / ?AMR-deprecated
references with proper {.topic AMR-options} / {.topic AMR-deprecated} cli markup
in count.R, interpretive_rules.R, proportion.R, and zz_deprecated.R.

Add {.topic} fallback handler to format_message() in aa_helper_functions.R:
plain-text environments render {.topic foo} as ?foo, and the [text](topic)
link form extracts just the display text (same pattern as {.help}).

Also convert remaining backtick function/arg references in proportion.R to
{.help [{.fun ...}](AMR::...)}, {.arg}, and {.code} markup for consistency.

Note: zzz.R intentionally keeps the backtick form since its startup message
goes through packageStartupMessage() which bypasses our cli infrastructure.

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b

R/interpretive_rules.R

@@ -1097,7 +1097,7 @@ eucast_rules <- function(x,
                          rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                          ...) {
   if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
-    warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.code ?AMR-options}.")
+    warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic AMR-options}.")
   }
   interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
 }