Add research methodology, critical thinking, and archive checkbox system

[jeremyandrews]

Summary

Combines two previously split PRs into one coherent change: comprehensive research guidelines + archive checkbox system.

Core Principles (JESSE.md)

• "Think critically, always" -- every analysis, fact-check, and recommendation must model critical thinking: question assumptions, identify gaps, name fallacies, show how to evaluate sources
• "Check the vault before going external" -- QMD search before web/external queries, scoped to cover research projects (not just person/project lookups)
• Research section update -- references three-layer devil's advocate, critical thinking, multilingual sourcing, and knowledge extraction into Knowledge/

Research-Guidelines.md (complete rewrite)

Replaces the minimal formatting-focused guidelines with a full research methodology:

• Vault first -- query QMD before any web search; reference vault context alongside external findings
• Scope confirmation -- confirm scope on ambiguous requests, skip on focused ones
• Writing quality -- narrative flow, no filler, specific over general (numbers, dates, names)
• Critical thinking -- question the premise, show reasoning not just conclusions, identify gaps, name fallacies naturally, give concrete examples
• Source hierarchy -- four-tier priority (primary > institutional > quality journalism > everything else with caveats), inline trustworthiness ratings
• Web search mandate -- training knowledge is not a citable source; every non-trivial fact must trace to a retrieved, dated, linkable source
• Multilingual sourcing -- mandatory for non-English contexts; "sparse in English" means you stopped too early
• Structural hints by research type -- patterns for technical, market/competitive, and domain research
• Devil's advocate (three layers) -- steelman the claim, best counterargument, nuanced resolution
• Stress-testing -- challenge assumptions rather than validate them; expand beyond narrow framing
• Handling conflicts and gaps -- distinguish fact/speculation/synthesis; resolve conflicts inline
• Pre-delivery quality check -- 5-point self-review checklist
• Report structure -- scope > executive overview > body > devil's advocate > summary > actionability > appendices > sources
• Archive footer -- references Archive-Footer-Guidelines for processing rules

Archive Checkbox System (from PR #10)

• Draft Lifecycle -- archive footer requirement integrated as closing paragraph (not standalone bold block)
• Archive Checkbox Processing -- grep-based detection (using grep -E for macOS compatibility), subagent delegation workflow, efficiency constraints
• Archive-Footer-Guidelines.md (new file) -- three checkbox options (Archive, Deep extract, Archive only), processing rules, grep pattern, hyphen-style standardization
• Vault Structure -- added Archive-Footer-Guidelines.md to listing

Vault-Search-Guidelines.md

• Reinforces that QMD applies equally to research tasks, not just file lookups

Review feedback addressed

• Archive footer rule flows naturally within Draft Lifecycle instead of abrupt standalone block
• Paths noted as deployment-adjustable (not hardcoded)
• Check frequency made dynamic instead of "maybe four times a day"
• Fixed "two run" → "to run" and "inneficient" → "inefficient" typos
• All-three-checked behavior: reports error to user instead of silent no-op
• grep uses -E (ERE) for macOS/BSD portability
• Hyphen-style list markers documented as the standard

Test plan

• JESSE.md Core Principles has both new bullet points (critical thinking, vault-first)
• JESSE.md Draft Lifecycle ends with archive footer requirement
• JESSE.md Archive Checkbox Processing section uses grep -E pattern
• JESSE.md Vault Structure lists Archive-Footer-Guidelines.md
• Research-Guidelines.md covers all methodology sections
• Research-Guidelines.md archive footer section references Archive-Footer-Guidelines
• Archive-Footer-Guidelines.md has all three checkbox options
• Archive-Footer-Guidelines.md uses grep -E pattern
• Archive-Footer-Guidelines.md says to report (not silently handle) all-three-checked
• Vault-Search-Guidelines.md includes research-scoped guidance
• No unrelated sections modified

[jeffsheltren]

LGTM. I added a commit with my local improvements as well