Removing several occurrences of this typo in the docs and javadocs, seems to be
a common mistake. Corrections turn up once in a while in PRs, better to correct
some of this in one sweep.
Links to inner classes were using `$` in urls instead of `.`, causing
them to 404.
Also fixes the doc generation code to generate docs into the correct
directory. We moved the docs but never updated the generation code.
This commit adds back "id" as the key within a script to specify a
stored script (which with file scripts now gone is no longer ambiguous).
It also adds "source" as a replacement for "code". This is in an attempt
to normalize how scripts are specified across both put stored scripts and script usages, including search template requests. This also deprecates the old inline/stored keys.