Replace PHP scripts with R or Java

[nichtich]

The source contains some of PHP, mainly for simple tasks:

wc -l $(git ls-files | grep .php)
  228 scripts/cli-generator/generate.php
   46 scripts/shelf-ready/shelf-ready-histogram.php
   32 scripts/sqlite/normalize-issue-details.php
   54 scripts/sqlite/solr-copy-ids-from-validation.php
  113 scripts/sqlite/validation-result-indexer-grouped.php
   64 scripts/sqlite/validation-result-indexer-simple.php
   46 scripts/tt-histogram/tt-histogram.php
   62 scripts/utils/parameter-filter.php
  645 total

Compared to 2.562 lines of Shell, 2.637 lines of R 118.459 lines of Java this is little, so rewriting in one of these languages seems doable to improve maintability and code quality (Java is already covered by tests/code analysis but R, Shell and PHP is not).