tantale 0.99.0 (release candidate)

Release candidate for tantale 1.0.0, submitted for rOpenSci review
(pre-submission inquiry: ropensci/software-review#813).

The interface is declared stable: from 1.0.0 on, changes to it follow the
lifecycle conventions (deprecation before removal).

Highlights since the prototype:

• tell_tales() finds TALE genes in genome assemblies, including
  error-prone long-read ones, and can correct frameshifts.
• TALEs are held in S3 classes (tales, tales_msa, pairwise_distances)
  with methods to validate, subset, combine, align and plot them.
• Repeat-level alignment, the DisTAL and FuncTAL distances, and grouping
  into families.
• Wrappers for AnnoTALE (now including assignment to its published TALE
  classes), TALEcorrection, PrediTALE and TALVEZ.
• tale_annotations: 128 curated TALEs from ten published
  Xanthomonas oryzae genomes.

Install this version with:

pak::pkg_install("scunnac/tantale@v0.99.0")

then run tantale::tantale_setup(install = TRUE) once to build the conda
environment and download the Java tools and example genomes (the
tools-1 and genomes-1 releases).

Full list of changes: NEWS.md. Documentation: https://scunnac.github.io/tantale/

tantale tools, version 1

Java programs wrapped by tantale (AnnoTALE 1.5, PrediTALE, TALEcorrection with its HMMs), with licence, provenance and per-file sha256. Downloaded by tantale::tantale_setup(install = TRUE); never modified after publication. sha256 of the archive: 6ebdfbfe66e269fcdb1285b64f06dffaf30f466ef3c234f6a90e81d089627501

tantale example genomes, version 1

Four Xanthomonas oryzae pv. oryzae genomes used by the tantale articles (MAI1 CP025609.1, BAI3 CP025610.1, PXO86 NZ_CP007166.1, BAI3-1-1). Downloaded by tantale::tantale_setup(install = TRUE); never modified after publication. sha256 of the archive: f7eb357025fbabec836b6b58323bcfa692319b94de989d303f79f0b963105ff4

Git bundle of the prototype v0.9.9004

Minor code reindent and notes_for_claude.md