docs: backfill missing project documentation

[iamlasse]

Summary

Backfills the standard project-level documentation that was missing from the repo. The Go code itself is already fully documented (all exported decls have doc comments; only 1 of 24 packages lacked a // Package doc), so this PR targets the project artifacts rather than code comments.

Changes

• CONTRIBUTING.md (new) — prerequisites, the dev loop via make targets (build, test, test-race, coverage, lint), the pre-commit hook (make install-hooks → gofmt/go vet/go build, bypass via --no-verify), branch + PR workflow, and the required commit-trailer convention (Nightshift-Task / Nightshift-Ref). Grounded in the existing Makefile, scripts/pre-commit.sh, and the README Development section.
• ARCHITECTURE.md (new) — module overview, the cmd/ layer, and the internal/ packages grouped by responsibility (config/state/db, agents/providers/integrations, tasks/scheduler/orchestrator, budget/calibration feedback loop, security, observability, analysis, projects/setup). Package descriptions are taken from each package's own doc comment; dependency edges are verified from imports. References docs/guides/run-lifecycle.md for the runtime flow rather than duplicating it. Inferred relationships are explicitly flagged as assumptions.
• cmd/provider-calibration/main.go — added the missing // Command provider-calibration package doc (the only package of 24 lacking one), describing it as the standalone diagnostic tool that aggregates Codex/Claude session metrics to suggest a budget-calibration multiplier.
• website/docs/cli-reference.md — audited against the actual cobra command tree and backfilled genuine gaps: added the missing top-level commands (config, init, report, install, uninstall, busfactor) to the command table, and added new Configuration Commands and Daemon Commands sections documenting the config get/set/validate and daemon start/stop/status subcommands and their flags.

Verification

• gofmt -l . → empty
• go vet ./... → clean
• go build ./... → clean
• go test ./... → all pass
• go doc ./cmd/provider-calibration → new package doc renders

Notes

• No internal/sandbox or internal/ui package exists; references to a sandbox layer were treated as non-existent (not fabricated).
• Markdown docs are intentionally grounded in existing tooling and source to keep hallucination risk low; inferred architectural relationships in ARCHITECTURE.md are marked as assumptions.

Nightshift-Task: docs-backfill
Nightshift-Ref: https://github.com/marcus/nightshift