feat: surface quality/lifecycle commands in prime, template, and doctor

[seanmartinsmith]

Summary

Surfaces existing but undiscoverable commands in prime output (CLI mode) and
the beads-section.md template. Adds doctor --check=conventions as a composite
of existing checks (lint + stale + orphans). No new commands or behavior -
just visibility for what's already there.

MCP mode and beads-section-minimal.md are unchanged.

Context

#2611 and #2612 documented the discoverability gap from the command/flag
alias angle - agents trying intuitive names that don't match. #2639 and
#2638 address that by adding aliases so wrong guesses work.

this PR addresses the other side: agents that never try commands they don't
know exist. dogfooding on 100's of beads showed bd prime surfaces ~19 of 100+
commands. result: --acceptance never used, --validate unknown, bd human
reinvented manually, 26% of close reasons were terse one-liners.

this fix is adding bullet points to prime and the template - surfacing
features, not adding them. doctor --check=conventions wraps three existing
commands (bd lint, bd stale, bd orphans) into one pass, advisory only.

Changes

two commits, independently cherry-pickable:

1. prime + template - adds Quality Tools, Lifecycle & Hygiene, Structured
   Workflows, and Close Reason Format sections to CLI prime output.
   beads-section.md gets a condensed version for non-hook agents.
2. doctor --check=conventions - composite check using existing lint,
   stale (14-day threshold), and orphan detection. warns, never blocks.
   follows the existing doctorCheck pattern.

Test plan

• bd prime --full shows new sections, bd prime --mcp unchanged
• bd doctor --check=conventions runs without error (supports --json)
• script test prime_content.txt, 3 unit tests for conventions check
• beads-section-minimal.md unchanged

[seanmartinsmith]

related: #2654 fixes --validate to check the --acceptance field and adds validation.on-close config

[steveyegge]

Most of this is good — surfacing existing commands in prime and the template is worthwhile, and doctor --check=conventions is a clean composition of existing checks.

However, the Close Reason Format section needs to come out:

## Close Reason Format
When closing non-trivial work, structure the reason:
Summary: [one line - what was done]
Change: [what changed and why]
Files: [key files modified]
Discovery: [what was learned that wasn't known at start]

This is a convention nobody follows yet — actual close reasons in our DB are mostly "Closed" or brief sentences. Injecting a prescriptive template into every agent's prime context burns tokens for a format with zero adoption. If we want structured close reasons, the path is:

1. Discuss the convention as a team
2. Use validation.on-close from your other PR (fix: --validate checks --acceptance field, add validation.on-close config #2654) to nudge toward it
3. Only add it to prime once it's an established convention, not to bootstrap one

Please remove the Close Reason Format block from prime.go and the "Structure close reasons: Summary + Change + Files + Discovery" line from beads-section.md, then this is ready for another look.