Revert "Issue #1367000 by chris.leversuch, oriol_e9g, David_Rothstein: Clean up API docs for php module."

Sorry, we're over thresholds atm. Hopefully can commit this soon.

This reverts commit 4303ae6e48e140696e1a9c923bcdf913fa63c88d.
Issue #278425 by andypost, droplet, OnkelTem, chx, c960657, drewish, kotnik, realityloop: Change notice for: Using basename() is not locale safe.
Issue #1402962 by xjm, marcingy, oriol_e9g, msonnabaum: Fixed Render cache shouldn't treat empty strings as a cache miss.
Issue #1386976 by nburles, LSU_JBob: Fixed Bug in drupal.js when minified.
Issue #1373582 by jhodgdon, TR: Fixed Trailing whitespace.
Issue #987930 by David_Rothstein, Tor Arne Thune: Fixed The obsolete 'site_offline_message' variable is not always deleted during the D6->D7 upgrade.
Issue #1160928 follow-up by sun: Commit missing file. Oops.
- Patch #1330554 by oriol_e9g, fiftyz, richthegeek: Fixed taxonomy_get_tree() incorrect depth on multiple parents.
- Patch #1386514 by pflame, nod_, David_Rothstein: Fixed Dragging and dropping a shortcut from disabled to enabled doesn't switch the status if the dragging happens fast.
- Patch #666854 by TR, JacobSingh: fixed E_NOTICE warnings in run_tests().sh .
- Patch #1000074 by naxoc: node_permission() uses check_plain() without a purpose.
- Patch #1387098 by LSU_JBob, nburles: bug in ajax.js when minified.
- Patch #1387572 by pbull, tarekdj: Fixed node links are not left aligned in bartik theme on RTL direction.
- Patch #1346166 by Dave Reid: Improve performance of token_replace() if there are no tokens to replace.
- Patch #736556 by daniels220, jeckman, Albert Volkman: fixed theme_links() doc needs expansion.
- Patch #1416218 by scorchio: Improve variable naming in format_interval().
- Patch #852524 by plach, oriol_e9g: include language provider files only when they are needed.
- Patch #1377544 by kotnik: hook_update_N documentation uses dead links.
- Patch #1394790 by joachim: explain system_admin_compact_mode().
- Patch #1354852 by marvil07, 30equals: hook_node_type_insert() has no sample function body.