docs: settle open design items + dogfood backlog

Resolve the five design-session open items from PLAN.md:
- decisions.md: soft write-path, poll-only sync (NAT), lognormal
  cold-start priors, purity test binds the SQLite cache
- pm-state.md: sidecar layout + directive/capacity/calibration
  schemas + lifecycle inference table
- agent-tools.md: query_project read tool + three write tools

Also gitignore .env.* (protect the gitea PAT) and record the P0
actual: 10 labels, 5 milestones, 34 tracer-bullet issues + 51
dependencies filed on christian/commitea as the first managed project.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.gitignore

@@ -4,6 +4,8 @@ out/
 *.log
 .DS_Store
 .env
+.env.*
+!.env.example
 .yarn/*
 !.yarn/patches
 !.yarn/plugins