docs: enforce issue-driven verified workflow

[dkritarth]

Closes #48

User outcome

Agents now receive one authoritative, phased GitHub Issue at a time, with explicit dependency locks and verification requirements tied to Kritarth's real Ph.D. paper-reading workflow.

Scope

• Makes GitHub Issues sole executable backlog; PLAN remains product context and wiki becomes historical archive.
• Adds personal project goal, Codex-first priority, sub-agent accountability, live Electron verification, and PR evidence contract.
• Adds structured issue form and PR template.
• Adds CI issue gate requiring exactly one closing issue, allowed active status, and complete verification sections.
• Updates wiki submodule to pushed archive commit 377aafe.
• Creates labels, four milestones, and detailed issues [S0-01] Prove Codex ACP against current signed-in subscription #25–[G3] Gate: certify advanced research workflow #47.
• Links and blocks existing stacked PRs P2-01: Notes tab — per-paper markdown notes (SQLite) #21–P2-04: ORCID author badges #24 against issues [R1-01] Verify and finish per-paper Notes workflow #29–[R1-04] Verify and finish ORCID author evidence #32.

Non-goal: this PR does not claim current application flows work. Issue #25 starts live product verification.

Acceptance criteria

• Root docs identify GitHub Issues as sole task authority.
• Exactly issue [S0-01] Prove Codex ACP against current signed-in subscription #25 is ready; [S0-02] Audit complete real-paper Electron journey and record every failure #26–[G3] Gate: certify advanced research workflow #47 are blocked.
• Issues carry milestones, blockers, acceptance criteria, live procedures, and evidence.
• PRs P2-01: Notes tab — per-paper markdown notes (SQLite) #21–P2-04: ORCID author badges #24 close correct issues and preserve stacked order.
• New issue form defaults work to blocked.
• CI gate rejects blocked, unlinked, or structurally under-evidenced PRs.
• Wiki archive update is pushed.
• YAML and Markdown/diff checks pass.
• After merge, master branch protection requires issue-gate status.

Automated verification

• YAML parse: all .github/**/*.yml
• Focused governance queries: labels, milestones, issues [S0-01] Prove Codex ACP against current signed-in subscription #25–[OPS-01] Make GitHub Issues the enforced source of truth #48, PRs P2-01: Notes tab — per-paper markdown notes (SQLite) #21–P2-04: ORCID author badges #24
• npm test — 143/143 passed across 24 files
• npm run typecheck
• npm run build
• git diff --check
• Wiki git diff --check

Live Electron verification

Not applicable to documentation/governance behavior. This PR deliberately does not certify Electron runtime. Issue #25 and subsequent Phase-0 issues require signed-in Codex and complete live Electron exercise before feature phases unlock.

Visual and console evidence

No visible product UI changed. Test suite emitted existing jsdom HTMLCanvasElement.prototype.getContext not-implemented stderr during Reader tests; suite still passed. This noise is not treated as live PDF rendering proof.

Real-paper / ACP evidence

Not run for this governance PR. No ACP or application behavior changed. Issue #25 requires real signed-in Codex smoke test and issue #26 requires real-paper Electron audit.

Limitations and follow-ups

GitHub issue labels and CI enforce PR eligibility; issue start order still depends on agents obeying status:blocked. Branch protection will require new check after workflow reaches master. Existing PRs #21–#24 require current live evidence and must remain blocked.

Independent review

• Created GitHub objects were queried back after creation.
• Linked issue has status:verification, not status:blocked.
• Governance queries and required branch protection were repeated after merge.

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: c8c1f755-b607-438e-a18f-d1c379573b7f

📥 Commits

Reviewing files that changed from the base of the PR and between ef39911 and a24768f.

📒 Files selected for processing (10)

• .github/ISSUE_TEMPLATE/config.yml
• .github/ISSUE_TEMPLATE/vellum-task.yml
• .github/pull_request_template.md
• .github/workflows/issue-gate.yml
• AGENTS.md
• CLAUDE.md
• HANDOFF.md
• PLAN.md
• README.md
• Vellum.wiki

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch codex/github-issue-backlog

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