find_sprinzl_id() assumes nuc- prefix not present in bundled coords

[jmbilodeaux]

Summary

find_sprinzl_id() in R/identity.R builds its search pattern as:

pattern <- paste0("^nuc-", rna_name, "-")

The bundled E. coli, T4, T5, and S. cerevisiae Sprinzl coordinate
files (in inst/extdata/sprinzl/) use plain tRNA-... identifiers
with no prefix. The ^nuc- prefix is never present, so
find_sprinzl_id() always returns NULL for these organisms, causing
plot_identity_structure() and plot_identity_panel() to fail with
"No Sprinzl coordinate entry found" for any bundled dataset.

Minimal reproducible

# Using the bundled E. coli coords:
path <- system.file("extdata/sprinzl/ecoliK12_global_coords.tsv.gz",
                    package = "clover")
coords <- read_sprinzl_coords(path)
head(unique(coords$trna_id))
# [1] "tRNA-Ala-GGC-1-1" ...   ← no "nuc-" prefix

# find_sprinzl_id looks for "^nuc-tRNA-Ala-AGC-1-1-"  → NULL every time

Suggested fix

Make the prefix optional — try ^nuc- first, then fall back to
^tRNA-:

find_sprinzl_id <- function(trna, sprinzl_coords) {
  ...
  for (prefix in c("^nuc-", "^")) {
    pattern <- paste0(prefix, rna_name, "-")
    matches <- grep(pattern, ids, value = TRUE)
    if (length(matches) > 0) return(sort(matches)[1])
  }
  NULL
}

cc @jayhesselberth for review