v1.3.1

Three fixes from testing every command on a machine set up the ordinary way.

Reinstalling no longer deletes your files. The installer used to remove
scripts/, tests/ and reference/ before copying, which also removed anything
you had added there and your generated test cases. It now writes the shipped
files over the top and leaves everything else alone, and says what it changed:

updated   skill    ~/.claude/skills/recall
          0 new, 3 updated, 11 unchanged, 2 of your own file(s) left alone

Your index, notes, activity log and tuning live outside that directory and were
never involved either way.

The commands work from any terminal. python -m claude_rework now works
wherever Python does. If pip put the executable somewhere that is not on your
PATH, install and doctor detect it and print both the directory to add and
the module form to use instead. A PATH problem is reported as advice rather than
a failure, because the hooks and the MCP server use absolute interpreter paths
and never depended on PATH.

--digest no longer repeats itself. It took the three newest samples per
week, and overlapping chunks of one long message are not distinct, so the same
sentence could print three times.