analyze

name	analyze
description	Thorough analysis of code, architecture, or topics — produces a structured research report. Supports goal-based modes: Explore (general research), Audit (risk-focused critique), Improve (actionable suggestions), Custom (user-defined lens). Triggers: "analyze this code", "deep dive into", "research this topic", "investigate how X works", "audit this", "critique this", "suggest improvements", "find risks in".
version	3
tier	protocol

Thorough analysis of code, architecture, or topics — produces a structured research report.

Deep Research Protocol

Execute §CMD_EXECUTE_SKILL_PHASES.

Session Parameters

{
  "taskType": "ANALYSIS",
  "phases": [
    {"label": "0", "name": "Setup",
      "steps": ["§CMD_REPORT_INTENT", "§CMD_PARSE_PARAMETERS", "§CMD_SELECT_MODE", "§CMD_INGEST_CONTEXT_BEFORE_WORK"],
      "commands": [],
      "proof": ["mode", "sessionDir", "parametersParsed"],
      "gate": false},
    {"label": "1", "name": "Research Loop",
      "steps": ["§CMD_REPORT_INTENT"],
      "commands": ["§CMD_APPEND_LOG", "§CMD_TRACK_PROGRESS", "§CMD_ASK_USER_IF_STUCK"],
      "proof": ["logEntries", "keyFinding", "openGaps"]},
    {"label": "2", "name": "Calibration",
      "steps": ["§CMD_REPORT_INTENT", "§CMD_INTERROGATE"],
      "commands": ["§CMD_ASK_ROUND", "§CMD_LOG_INTERACTION"],
      "proof": ["depthChosen", "roundsCompleted"]},
    {"label": "3", "name": "Synthesis",
      "steps": ["§CMD_REPORT_INTENT", "§CMD_RUN_SYNTHESIS_PIPELINE"], "commands": [], "proof": [], "gate": false},
    {"label": "3.1", "name": "Checklists",
      "steps": ["§CMD_VALIDATE_ARTIFACTS", "§CMD_RESOLVE_BARE_TAGS", "§CMD_PROCESS_CHECKLISTS"], "commands": [], "proof": [], "gate": false},
    {"label": "3.2", "name": "Debrief",
      "steps": ["§CMD_GENERATE_DEBRIEF"], "commands": [], "proof": ["debriefFile", "debriefTags"], "gate": false},
    {"label": "3.3", "name": "Finding Triage",
      "steps": ["§CMD_WALK_THROUGH_RESULTS"], "commands": [], "proof": ["findingsTriaged", "delegated", "deferred", "dismissed"]},
    {"label": "3.4", "name": "Pipeline",
      "steps": ["§CMD_MANAGE_DIRECTIVES", "§CMD_PROCESS_DELEGATIONS", "§CMD_DISPATCH_APPROVAL", "§CMD_CAPTURE_SIDE_DISCOVERIES", "§CMD_RESOLVE_CROSS_SESSION_TAGS", "§CMD_MANAGE_BACKLINKS", "§CMD_MANAGE_ALERTS", "§CMD_REPORT_LEFTOVER_WORK"], "commands": [], "proof": [], "gate": false},
    {"label": "3.5", "name": "Close",
      "steps": ["§CMD_REPORT_ARTIFACTS", "§CMD_REPORT_SUMMARY", "§CMD_SURFACE_OPPORTUNITIES", "§CMD_OFFER_COUNCIL_REVIEW", "§CMD_OFFER_GRAPH_VIZ", "§CMD_CLOSE_SESSION", "§CMD_PRESENT_NEXT_STEPS"], "commands": [], "proof": ["reviewOffered", "decision", "graphOffered"], "gate": false}
  ],
  "nextSkills": ["/brainstorm", "/prove", "/implement", "/document", "/fix", "/chores"],
  "directives": [],
  "logTemplate": "assets/TEMPLATE_ANALYSIS_LOG.md",
  "debriefTemplate": "assets/TEMPLATE_ANALYSIS.md",
  "requestTemplate": "assets/TEMPLATE_ANALYSIS_REQUEST.md",
  "responseTemplate": "assets/TEMPLATE_ANALYSIS_RESPONSE.md",
  "modes": {
    "explore": {"label": "Explore", "description": "Broad, curiosity-driven investigation", "file": "modes/explore.md"},
    "audit": {"label": "Audit", "description": "Adversarial, risk-focused critique", "file": "modes/audit.md"},
    "improve": {"label": "Improve", "description": "Constructive, actionable suggestions", "file": "modes/improve.md"},
    "custom": {"label": "Custom", "description": "User provides framing, agent blends modes", "file": "modes/custom.md"}
  }
}

---

0. Setup

§CMD_REPORT_INTENT:

0: Analyzing ___. Trigger: ___. Focus: ___. Not: ___.

§CMD_EXECUTE_PHASE_STEPS(0.0.*)

• Scope: Understand the [Subject] and [Question] provided by the user.

Mode Selection (§CMD_SELECT_MODE):

On selection: Read the corresponding modes/{mode}.md file. It defines Role, Goal, Mindset, Research Topics, Calibration Topics, and Walk-Through Config.

On "Custom": Read ALL 3 named mode files first (modes/explore.md, modes/audit.md, modes/improve.md), then accept user's framing. Parse into role/goal/mindset.

Record: Store the selected mode. It configures:

• Phase 0 role (from mode file)
• Phase 1 research topics (from mode file)
• Phase 2 calibration topics (from mode file)
• Phase 3.3 walk-through config (from mode file)

---

1. Research Loop (Autonomous Deep Dive)

Do not wait for permission. Explore the context immediately.

§CMD_REPORT_INTENT:

1: Researching ___. ___. Focus: ___. Not: ___.

§CMD_EXECUTE_PHASE_STEPS(1.0.*)

A. Exploration Strategy

Iterate through the loaded files/docs using the Research Topics from the selected mode preset. Do not just read — Interrogate.

B. The Logging Stream (Your Primary Output)

For every significant thought, execute §CMD_APPEND_LOG. Logging is the core activity of analysis — without rich log entries, downstream synthesis and the final report will be shallow and uninformative.

• High Volume: Aim for 10-30 log entries per session. More is better.
• A thin log leads to a thin report. The log IS the raw material for everything downstream — the debrief, the finding triage, the action items. Every unlogged thought is a lost insight.
• Cadence: Log at least 8 items before moving to Calibration.
• Variety: Use ALL available log schemas (Discovery, Weakness, Connection, Spark, Gap, Pattern, Tradeoff, Assumption, Strength). Varied entry types produce richer analysis.

---

2. Calibration (Interactive)

After you have logged a significant batch of findings (8+), STOP and turn to the user.

Calibration is a fork, not a terminus. Its job is not merely to polish the write-up — it is to decide whether the analysis is done, or whether open gaps deserve another research pass. Treat the openGaps from Phase 1 as live: calibration either closes them (with the user) or routes them into a deepen loop (see §ASK_CALIBRATION_EXIT). Do not drift to Synthesis by default.

§CMD_REPORT_INTENT:

2: Calibrating with ___ findings logged. ___. Focus: ___. Not: ___.

§CMD_EXECUTE_PHASE_STEPS(2.0.*)

Findings Summary: Before asking any calibration questions, present a condensed summary of what was found during the Research Loop. Format as a numbered list of key findings (one line each), grouped by log entry type. This gives the user context to calibrate effectively — they can't guide the analysis if they don't know what was found.

Action: Present the findings summary, then ask the user to choose calibration depth. Then execute rounds.

Calibration Topics

Draw from the Calibration Topics defined in the selected mode preset. Universal repeatable topics (Followup, Devil's advocate, What-if, Deep dive) are available in all modes.

¶ASK_CALIBRATION_EXIT

Extends: §ASK_INTERROGATION_EXIT Trigger: after minimum calibration rounds are met Extras: A: Walk through findings so far | B: Go back to a previous topic | C: Show the open gaps

A forward fork, not a default-to-write-up. The real question here is: is the analysis done, or are there open gaps worth pursuing? Recommend by the state of openGaps (from Phase 1 proof + anything calibration surfaced) — gaps remain → recommend [DEEPEN]; gaps closed → recommend [NEXT]. Synthesizing is a deliberate "we've answered the question," never the lazy default. The old flow buried "more analysis" as a backward jump; here it is a first-class forward path.

Decision: Calibration Exit

• [NEXT] Synthesize now The analysis answers the question and no material gaps remain — proceed to Synthesis (write-up). Recommended only when openGaps is empty (or the user explicitly waives them).
• [DEEPEN] Pursue the open gaps Return to the Research Loop to investigate the outstanding openGaps, then re-enter Calibration. The forward path to more analysis — recommended when openGaps is non-empty.
• [COUNCIL] Panel on the analysis so far Convene a /council panel on the analysis-so-far to surface holes neither you nor the user caught. Its findings feed the DEEPEN loop, not the write-up.
• [MORE]
• [DEEP]
• Devil's advocate round
• What-if scenarios round
• Gaps round

On [NEXT]: transition to Phase 3 (Synthesis). In roundsCompleted, record the exit decision + the disposition of any open gaps (e.g. "exit=SYNTH; gaps: none outstanding" or "exit=SYNTH; 1 gap explicitly waived by user"). On [DEEPEN]: transition back to Phase 1 via engine session phase --user-approved (the reason MUST quote the user's choice, per ¶INV_USER_APPROVED_REQUIRES_TOOL). Carry the outstanding gaps forward as the Research Loop's focus. After Phase 1 completes, re-enter Phase 2 (Calibration) — re-calibration before Synthesis is mandatory; the deepen loop cannot skip it. On [COUNCIL]: invoke §CMD_OFFER_COUNCIL_REVIEW with subject session <dir> (the analysis-so-far — its log IS the findings record), report-only, offered not forced. When the panel's verdict lands, merge its MUST FIX / SHOULD FIX findings + blind_spots into openGaps, then re-present this same calibration exit — now with the panel's gaps in hand ([DEEPEN] will typically be recommended). Council drives reanalysis but never routes to Synthesis directly; it always returns here to re-gate. (This is distinct from the end-of-flow council in 3.5 Close, which QAs the finished report.)

---

3. Synthesis

When the user is satisfied.

§CMD_REPORT_INTENT:

3: Synthesizing. ___ findings logged, ___ calibration rounds completed. Focus: ___. Not: ___.

§CMD_EXECUTE_PHASE_STEPS(3.0.*)

Debrief notes (for ANALYSIS.md):

• Synthesize: Don't just summarize. Connect the dots between Log entries.
• Identify Themes: Group isolated findings into "Strategic Themes".
• Highlight: Top Risks and Sparks.
• Recommend: Concrete next steps.

3.3. Finding Triage (Action Planning)

Convert analysis into action. Walk through each finding with the user and decide its fate.

§CMD_REPORT_INTENT:

3.3: Triaging ___ findings into action items. Focus: ___. Not: ___.

§CMD_EXECUTE_PHASE_STEPS(3.3.*)

Execute §CMD_WALK_THROUGH_RESULTS with the Walk-Through Config from the selected mode preset.

Walk-through config:

§CMD_WALK_THROUGH_RESULTS Configuration:
  (uses Walk-Through Config from the selected mode preset)

Before closing, offer a /council panel review on the report doc <ANALYSIS.md> via §CMD_OFFER_COUNCIL_REVIEW (offer, not force) -- diverse expert eyes on the findings before they drive decisions. Then offer a /graph flowgraph of the analyzed algorithm / control flow / structure via §CMD_OFFER_GRAPH_VIZ (offer, context-gated -- skips linear artifacts).

Post-Synthesis: If the user continues talking (without choosing a skill), obey §CMD_RESUME_AFTER_CLOSE.