deep-reflect

name	deep-reflect
description	Deep research over the Egregore org memory — multi-hop, evidence-verified synthesis of what the org collectively knows — when the user invokes /deep-reflect or $deep-reflect.

Egregore Deep Reflect (v4)

Native Codex Egregore skill. Ask the org's memory a question and return a verified, cited synthesis of what it collectively knows — including what it doesn't. /reflect captures user thought; /deep-reflect researches what the org already knows.

Full contracts live in .claude/skills/deep-reflect/ (SKILL.md entry, RESEARCH.md engine, ROLES.md agent roles, REPORT.md output). Follow them; this file is the Codex-runtime adapter.

Modes

• Question (default): interrogative or bare-topic arguments → "what does the org know about X?"
• Cross-ref: "cross-reference this" / a declarative insight → "how does this insight sit against existing memory?"
• Depth: --brief (1 hop wave), standard (≤3), --deep (≤5). Default is dynamic from the corpus probe.

Flow

1. Check egregore.json mode FIRST. Local mode: full engine over files; never call graph, batch-graph, or notification scripts; zero graph vocabulary in output. Connected: graph adds hop rails and writeback, every graph call non-fatal (2>/dev/null || true).
2. FRAME: corpus probe — 2× bin/agent.sh search "$TOPIC" --fast -n 20 with different wordings + bin/artifacts.sh find "$TOPIC" + grep -ril "$TOPIC" memory/knowledge/ memory/handoffs/ memory/artifacts/. N = the union of unique paths; set the wave budget from N per RESEARCH.md §Budget; decompose the question into 2-4 sub-questions; print a plan line (Researching: … · ~N relevant docs · budget M waves · est ~X min). Under ~5 relevant docs: say memory is too thin and offer /reflect or /harvest instead of faking research. If search errors or returns nothing while grep hits, rely on grep and note "recall degraded".
3. SEED: check memory/knowledge/research/ for prior runs on the topic — their cited artifacts (frontmatter artifacts_cited, older reports use artifacts_consulted; resolve filename stems with find) are pre-warmed leads, and their null_regions gaps get re-audited. Build a frontier of ≤12 docs from search probes, frontmatter topic/quest greps, and index ledgers.
4. HOP WAVES: the Codex runtime has no Workflow tool — run the foreground staged path from ROLES.md: per wave, read 8-12 docs (subagents if the session offers them, otherwise staged single-model passes), extract claims-with-verbatim-excerpts and typed leads (doc links, quests, people, sessions, topic terms, named absences). Dedup against the seen-set, score leads, hop until saturation per RESEARCH.md (coverage on every sub-question plus low novelty or zero yield; or budget).
5. PATTERN: two de-correlated passes. Without subagents true blindness is impossible — degrade deliberately: run the TENSION pass FIRST (grouped by topic), then the convergence pass (chronological), so tension-finding is never anchored by an existing convergence story. Disagreement between passes is a finding, never averaged away.
6. VERIFY: for every claim, whitespace-normalize the excerpt and re-find it in the cited file (miss = miscite = kill; supported paraphrase = correct the excerpt). The mechanical re-check survives self-verification — it is a grep, not a judgment. Re-attack every gap claim with one extra probe; a found doc refutes the gap and joins the ledger. Evidence older than ~90 days gets one --fast newer-artifact probe. Report the kill count. When the verifying context is the same one that made the claims, mark the report's provenance verification: self-checked.
7. SYNTHESIZE + PRESENT: stance, not summary — answer first, then ◆ primary / ◇ secondary findings with memory/... path citations, tensions, and "what memory doesn't hold" (gaps + the probes that prove them). Confidence is derived from evidence structure (verified + ≥3 independent sources = high; single-source always labeled). Register: analyst, not critic.
8. CAPTURE (user-gated): Save (default) / Edit first / File follow-ups / Skip. On Save write memory/knowledge/research/YYYY-MM-DD-author-slug.md with frontmatter (question, mode, stop_reason, waves, docs_read, claims_killed, builds_on, artifacts_consulted, artifacts_cited, null_regions), then connected-mode best-effort graph writes per the main REPORT.md §Writeback (MERGE with filePath — do NOT use graph-op.sh register-artifact; RELATES_TO/TENSION_WITH for verified cross-ref claims only), then bin/agent.sh save --message "Deep research: $TOPIC" --topic "$TOPIC". On Skip: nothing is written except the local run ledger under .egregore/research-runs/. Render the TUI box AFTER the gate, reflecting the actual outcome.

Output

Render the Egregore deep-reflect confirmation TUI after the capture gate:

• 72-column outer box, standard top/separator/content/bottom lines only.
• Header: ◈ DEEP REFLECT, author, date.
• Body: question, ◆/◇ finding counts, confidence, waves · docs read · cited · claims cut in verification.
• Footer: actual saved/pushed state; say "graphed" only if the graph write succeeded; in local mode omit graph language entirely.
• Structured UX parity is required: preserve the rendered deep-reflect TUI box, no preamble, no prose-only replacement, and no raw search or graph output.
• Never show raw graph JSON; never replace the box with prose.

Rules

• Search budget: at most ONE non---fast search probe per run (seed only); --fast everywhere else. Count result blocks, never the banner hit count.
• No claim without a verbatim excerpt that survives re-finding in the file.
• Absence is a first-class finding — cite the probes that prove it.
• Don't manufacture significance: "memory holds nothing structural on this" is a valid report.
• At most ONE clarifying question before the run, plus the capture gate.
• Do not use Claude Code commands.