Deep Analysis

Deep Analysis Workflow

Execute a structured exploration + synthesis workflow using Agent Teams with hub-and-spoke coordination. The lead performs rapid reconnaissance to generate dynamic focus areas, composes a team plan for review, workers explore independently, and a synthesizer merges findings with Bash-powered investigation.

This skill can be invoked standalone or loaded by other skills as a reusable building block. Approval behavior is configurable via .claude/agent-alchemy.local.md.

Settings Check

Goal: Determine whether the team plan requires user approval before execution.

1. Read settings file:

   • Check if .claude/agent-alchemy.local.md exists
   • If it exists, read it and look for a deep-analysis section with nested settings:

     - **deep-analysis**:
       - **direct-invocation-approval**: true
       - **invocation-by-skill-approval**: false
     

   • If the file does not exist or is malformed, use defaults (see step 4)

2. Determine invocation mode:

   • Direct invocation: The user invoked /deep-analysis directly, or you are running this skill standalone
   • Skill-invoked: Another skill (e.g., codebase-analysis, feature-dev, docs-manager) loaded and is executing this workflow

3. Resolve settings:

   • If settings were found, use them as-is
   • If the file is missing or the deep-analysis section is absent, use defaults:
     • direct-invocation-approval: true
     • invocation-by-skill-approval: false
   • If the file exists but is malformed (unparseable), warn the user and use defaults

4. Set REQUIRE_APPROVAL:

   • If direct invocation → use direct-invocation-approval value (default: true)
   • If skill-invoked → use invocation-by-skill-approval value (default: false)

5. Parse session settings (also under the deep-analysis section):

   - **deep-analysis**:
     - **cache-ttl-hours**: 24
     - **enable-checkpointing**: true
     - **enable-progress-indicators**: true
   

   • cache-ttl-hours: Number of hours before exploration cache expires. Default: 24. Set to 0 to disable caching entirely.
   • enable-checkpointing: Whether to write session checkpoints at phase boundaries. Default: true.
   • enable-progress-indicators: Whether to display [Phase N/6] progress messages. Default: true.

6. Set behavioral flags:

   • CACHE_TTL = value of cache-ttl-hours (default: 24)
   • ENABLE_CHECKPOINTING = value of enable-checkpointing (default: true)
   • ENABLE_PROGRESS = value of enable-progress-indicators (default: true)

Phase 0: Session Setup

Goal: Check for cached exploration results, detect interrupted sessions, and initialize the session directory.

Skip this phase entirely if CACHE_TTL = 0 AND ENABLE_CHECKPOINTING = false.

Step 1: Exploration Cache Check

If CACHE_TTL > 0:

1. Check if .claude/sessions/exploration-cache/manifest.md exists
2. If found, read the manifest and verify:
   • analysis_context matches the current analysis context (or is a superset)
   • codebase_path matches the current working directory
   • timestamp is within CACHE_TTL hours of now
   • Config files referenced in config_checksum haven't been modified since the cache was written (check mod-times of package.json, tsconfig.json, pyproject.toml, etc.)
3. If cache is valid:
   • Skill-invoked mode: Auto-accept the cache. Set CACHE_HIT = true. Read cached synthesis.md and recon_summary.md. Skip to Phase 6 step 2 (present/return results).
   • Direct invocation: Use AskUserQuestion to offer:
     • "Use cached results" — Set CACHE_HIT = true, skip to Phase 6 step 2
     • "Refresh analysis" — Set CACHE_HIT = false, proceed normally
4. If cache is invalid or absent: Set CACHE_HIT = false

Step 2: Interrupted Session Check

If ENABLE_CHECKPOINTING = true:

1. Check if .claude/sessions/__da_live__/checkpoint.md exists
2. If found, read the checkpoint to determine last_completed_phase
3. Use AskUserQuestion to offer:
   • "Resume from Phase [N+1]" — Load checkpoint state, proceed from the interrupted phase (see Session Recovery in Error Handling)
   • "Start fresh" — Archive the interrupted session to .claude/sessions/da-interrupted-{timestamp}/ and proceed normally
4. If not found: proceed normally

Step 3: Initialize Session Directory

If ENABLE_CHECKPOINTING = true AND CACHE_HIT = false:

1. Create .claude/sessions/__da_live__/ directory
2. Write checkpoint.md:

   ## Deep Analysis Session
   - **analysis_context**: [context from arguments or caller]
   - **codebase_path**: [current working directory]
   - **started**: [ISO timestamp]
   - **current_phase**: 0
   - **status**: initialized
   

3. Write progress.md:

   ## Deep Analysis Progress
   - **Phase**: 0 of 6
   - **Status**: Session initialized
   
   ### Phase Log
   - [timestamp] Phase 0: Session initialized
   

Phase 1: Reconnaissance & Planning

Goal: Perform codebase reconnaissance, generate dynamic focus areas, and compose a team plan.

If ENABLE_PROGRESS = true: Display "[Phase 1/6] Reconnaissance & Planning — Mapping codebase structure..."

1. Determine analysis context:

   • If $ARGUMENTS is provided, use it as the analysis context (feature area, question, or general exploration goal)
   • If no arguments and this skill was loaded by another skill, use the calling skill's context
   • If no arguments and standalone invocation, set context to "general codebase understanding"
   • Set PATH = current working directory
   • Inform the user: "Exploring codebase at: PATH" with the analysis context

2. Rapid codebase reconnaissance: Use Glob, Grep, and Read to quickly map the codebase structure. This should take 1-2 minutes, not deep investigation.

   • Directory structure: List top-level directories with Glob (e.g., */ pattern) to understand the project layout
   • Language and framework detection: Read config files (package.json, tsconfig.json, pyproject.toml, Cargo.toml, go.mod, etc.) to identify primary language(s) and framework(s)
   • File distribution: Use Glob with patterns like src/**/*.ts, **/*.py to gauge the size and shape of different areas
   • Key documentation: Read README.md, CLAUDE.md, or similar docs if they exist for project context
   • For feature-focused analysis: Use Grep to search for feature-related terms (function names, component names, route paths) to find hotspot directories
   • For general analysis: Identify the 3-5 largest or most architecturally significant directories

   Fallback: If reconnaissance fails (empty project, unusual structure, errors), use the static focus area templates from Step 3b.

3. Generate dynamic focus areas:

   Based on reconnaissance findings, create focus areas tailored to the actual codebase. Default to 3 focus areas, but adjust based on codebase size and complexity (2 for small projects, up to 4 for large ones).

   a) Dynamic focus areas (default):

   Each focus area should include:

   • Label: Short description (e.g., "API layer in src/api/")
   • Directories: Specific directories to explore
   • Starting files: 2-3 key files to read first
   • Search terms: Grep patterns to find related code
   • Complexity estimate: Low/Medium/High based on file count and apparent structure

   For feature-focused analysis, focus areas should track the feature's actual footprint:

   Example:
   Focus 1: "API routes and middleware in src/api/ and src/middleware/" (auth-related endpoints, request handling)
   Focus 2: "React components in src/pages/profile/ and src/components/user/" (UI layer for user profiles)
   Focus 3: "Data models and services in src/db/ and src/services/" (persistence and business logic)
   

   For general analysis, focus areas should map to the codebase's actual structure:

   Example:
   Focus 1: "Next.js app layer in apps/web/src/" (pages, components, app router)
   Focus 2: "Shared library in packages/core/src/" (utilities, types, shared logic)
   Focus 3: "CLI and tooling in packages/cli/" (commands, configuration, build)
   

   b) Static fallback focus areas (only if recon failed):

   For feature-focused analysis:

   Focus 1: Explore entry points and user-facing code related to the context
   Focus 2: Explore data models, schemas, and storage related to the context
   Focus 3: Explore utilities, helpers, and shared infrastructure
   

   For general codebase understanding:

   Focus 1: Explore application structure, entry points, and core logic
   Focus 2: Explore configuration, infrastructure, and shared utilities
   Focus 3: Explore shared utilities, patterns, and cross-cutting concerns
   

4. Compose the team plan:

   Assemble a structured plan document from the reconnaissance and focus area findings:

   ## Team Plan: Deep Analysis
   
   ### Analysis Context
   [context from Step 1]
   
   ### Reconnaissance Summary
   - **Project:** [name/type]
   - **Primary language/framework:** [detected]
   - **Codebase size:** [file counts, key directories]
   - **Key observations:** [2-3 bullets]
   
   ### Focus Areas
   
   #### Focus Area 1: [Label]
   - **Directories:** [list]
   - **Starting files:** [2-3 files]
   - **Search patterns:** [Grep patterns]
   - **Complexity:** [Low/Medium/High]
   - **Assigned to:** explorer-1 (sonnet)
   
   #### Focus Area 2: [Label]
   - **Directories:** [list]
   - **Starting files:** [2-3 files]
   - **Search patterns:** [Grep patterns]
   - **Complexity:** [Low/Medium/High]
   - **Assigned to:** explorer-2 (sonnet)
   
   [... repeated for each focus area]
   
   ### Agent Composition
   | Role | Count | Model | Purpose |
   |------|-------|-------|---------|
   | Explorer | [N] | sonnet | Independent focus area exploration |
   | Synthesizer | 1 | opus | Merge findings, deep investigation |
   
   ### Task Dependencies
   - Exploration Tasks 1-[N]: parallel (no dependencies)
   - Synthesis Task: blocked by all exploration tasks
   

5. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .claude/sessions/__da_live__/checkpoint.md: set current_phase: 1
   • Write .claude/sessions/__da_live__/team_plan.md with the full team plan from Step 4
   • Write .claude/sessions/__da_live__/recon_summary.md with reconnaissance findings from Step 2
   • Append to progress.md: [timestamp] Phase 1: Reconnaissance complete — [N] focus areas identified

Phase 2: Review & Approval

Goal: Present the team plan for user review and approval before allocating resources.

If ENABLE_PROGRESS = true: Display "[Phase 2/6] Review & Approval — Presenting team plan..."

If REQUIRE_APPROVAL = false

Skip to Phase 3 with a brief note: "Auto-approving team plan (skill-invoked mode). Proceeding with [N] explorers and 1 synthesizer."

If REQUIRE_APPROVAL = true

1. Present the team plan to the user (output the plan from Phase 1 Step 4), then use AskUserQuestion:

   • "Approve" — Proceed to Phase 3 as-is
   • "Modify" — User describes changes (adjust focus areas, add/remove explorers, change scope)
   • "Regenerate" — Re-run reconnaissance with user feedback

2. If "Modify" (up to 3 cycles):

   • Ask what to change using AskUserQuestion
   • Apply modifications to the team plan (adjust focus areas, agent count, scope)
   • Re-present the updated plan for approval
   • If 3 modification cycles are exhausted, offer "Approve current plan" or "Abort analysis"

3. If "Regenerate" (up to 2 cycles):

   • Ask for feedback/new direction using AskUserQuestion
   • Return to Phase 1 Step 2 with the user's feedback incorporated
   • Re-compose and re-present the team plan
   • If 2 regeneration cycles are exhausted, offer "Approve current plan" or "Abort analysis"

4. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .claude/sessions/__da_live__/checkpoint.md: set current_phase: 2, record approval_mode (approved/auto-approved)
   • Append to progress.md: [timestamp] Phase 2: Plan approved (mode: [approval_mode])

Phase 3: Team Assembly

Goal: Create the team, spawn agents, create tasks, and assign work using the approved plan.

If ENABLE_PROGRESS = true: Display "[Phase 3/6] Team Assembly — Creating team and spawning agents..."

1. Create the team:

   • Use TeamCreate with name deep-analysis-{timestamp} (e.g., deep-analysis-1707300000)
   • Description: "Deep analysis of [analysis context]"

2. Spawn teammates: Use the Task tool with the team_name parameter to spawn teammates based on the approved plan:

   • N explorers (one per focus area) — subagent_type: "code-explorer", model: sonnet

     • Named: explorer-1, explorer-2, ... explorer-N
     • Prompt each with: "You are part of a deep analysis team. Wait for your task assignment. The codebase is at: [PATH]. Analysis context: [context]"

   • 1 synthesizer — subagent_type: "code-synthesizer"

     • Named: synthesizer
     • Prompt with: "You are the synthesizer for a deep analysis team. You have Bash access for git history, dependency analysis, and static analysis. Wait for your task assignment. The codebase is at: [PATH]. Analysis context: [context]"

3. Create tasks: Use TaskCreate for each task based on the approved plan's focus areas:

   • Exploration Task per focus area: Subject: "Explore: [Focus area label]", Description: detailed exploration instructions including directories, starting files, search terms, and complexity estimate
   • Synthesis Task: Subject: "Synthesize and evaluate exploration findings", Description: "Merge and synthesize findings from all exploration tasks into a unified analysis. Investigate gaps using Bash (git history, dependency trees). Evaluate completeness before finalizing."
     • Use TaskUpdate to set addBlockedBy pointing to all exploration task IDs

4. Assign exploration tasks (with status guard):

   For each exploration task, apply the following status-guarded assignment:

   1. Use TaskGet to check the task's current status and owner
   2. Only assign if status is pending AND owner is empty
   3. If already assigned or completed: log "Task [ID] already [status], skipping" and move on
   4. Use TaskUpdate to set the owner to the corresponding explorer
   5. Send the explorer a message with the task details via SendMessage:

      SendMessage type: "message", recipient: "[explorer-N]",
      content: "Your exploration task [ID] is assigned. Focus area: [label]. Directories: [list]. Starting files: [list]. Search patterns: [list]. Begin exploration now.",
      summary: "Exploration task assigned"
      

   Never re-assign a completed or in-progress task.

5. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .claude/sessions/__da_live__/checkpoint.md: set current_phase: 3, record team_name, explorer_names (list), task_ids (map of explorer → task ID), synthesis_task_id
   • Append to progress.md: [timestamp] Phase 3: Team assembled — [N] explorers, 1 synthesizer

Phase 4: Focused Exploration

Goal: Workers explore their assigned areas independently.

If ENABLE_PROGRESS = true: Display "[Phase 4/6] Focused Exploration — 0/[N] explorers complete"

Monitoring Loop

After assigning exploration tasks, monitor progress with status-aware tracking:

1. When an explorer goes idle or sends a message, use TaskGet to check their task status
2. If task is completed: Record the explorer's findings. If ENABLE_CHECKPOINTING = true, write explorer-{N}-findings.md to .claude/sessions/__da_live__/ and update checkpoint.
3. If task is in_progress: The explorer is still working — do NOT re-send the assignment
4. If task is pending and owner is set: The explorer received the assignment but hasn't started yet — wait, do NOT re-send
5. If task is pending and owner is empty: Assignment may have been lost — re-assign using the status guard from Phase 3 step 4

Never re-assign a completed or in-progress task. This is the primary duplicate prevention mechanism.

If ENABLE_PROGRESS = true: Update the progress display as explorers complete: "[Phase 4/6] Focused Exploration — [completed]/[N] explorers complete"

• Workers explore their assigned focus areas independently — no cross-worker messaging
• Workers can respond to follow-up questions from the synthesizer
• Each worker marks its task as completed when done
• You (the lead) receive idle notifications as workers finish
• Wait for all exploration tasks to be marked complete before proceeding to Phase 5

Phase 5: Evaluation and Synthesis

Goal: Verify exploration completeness, launch synthesis with deep investigation.

If ENABLE_PROGRESS = true: Display "[Phase 5/6] Synthesis — Merging findings and investigating gaps..."

Step 1: Structural Completeness Check

This is a structural check, not a quality assessment:

1. Use TaskList to verify all exploration tasks are completed
2. Check that each worker produced a report with content (review the messages/reports received)
3. If a worker failed completely (empty or error output):
   • Create a follow-up exploration task targeting the gap
   • Assign it to an idle worker
   • Add the new task to the synthesis task's blockedBy list
   • Wait for the follow-up task to complete
4. If all produced content: proceed immediately to Step 2

Step 2: Launch Synthesis

1. Use TaskUpdate to assign the synthesis task: owner: "synthesizer"

2. Send the synthesizer a message with exploration context and recon findings:

   SendMessage type: "message", recipient: "synthesizer",
   content: "All exploration tasks are complete. Your synthesis task is now assigned.
   
   Analysis context: [analysis context]
   Codebase path: [PATH]
   
   Recon findings from planning phase:
   - Project structure: [brief summary of directory layout]
   - Primary language/framework: [what was detected]
   - Key areas identified: [the focus areas and why they were chosen]
   
   The workers are: [list of explorer names from the approved plan]. You can message them with follow-up questions if you find conflicts or gaps in their findings.
   
   You have Bash access for deep investigation — use it for git history analysis, dependency trees, static analysis, or any investigation that Read/Glob/Grep can't handle.
   
   Read the completed exploration tasks via TaskGet to access their reports, then synthesize into a unified analysis. Evaluate completeness before finalizing.",
   summary: "Synthesis task assigned, begin work"
   

3. Wait for the synthesizer to mark the synthesis task as completed

4. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .claude/sessions/__da_live__/checkpoint.md: set current_phase: 5
   • Write .claude/sessions/__da_live__/synthesis.md with the synthesis results
   • Append to progress.md: [timestamp] Phase 5: Synthesis complete

Phase 6: Completion + Cleanup

Goal: Collect results, present to user, and tear down the team.

If ENABLE_PROGRESS = true: Display "[Phase 6/6] Completion — Collecting results and cleaning up..."

1. Collect synthesis output:

   • The synthesizer's findings are in the messages it sent and/or the task completion output
   • Read the synthesis results

2. Write exploration cache (if CACHE_TTL > 0):

   • Create .claude/sessions/exploration-cache/ directory (overwrite if exists)
   • Write manifest.md:

     ## Exploration Cache Manifest
     - **analysis_context**: [the analysis context used]
     - **codebase_path**: [current working directory]
     - **timestamp**: [ISO timestamp]
     - **config_checksum**: [comma-separated list of config files and their mod-times]
     - **ttl_hours**: [CACHE_TTL value]
     - **explorer_count**: [N]
     

   • Write synthesis.md with the full synthesis output
   • Write recon_summary.md with the Phase 1 reconnaissance findings
   • Write explorer-{N}-findings.md for each explorer's findings (if not already persisted from Phase 4 checkpoints)

3. Present or return results:

   • Standalone invocation: Present the synthesized analysis to the user. The results remain in conversation memory for follow-up questions.
   • Loaded by another skill: The synthesis is complete. Control returns to the calling workflow — do not present a standalone summary.

4. Shutdown teammates: Send shutdown requests to all spawned teammates (iterate over the actual agents from the approved plan):

   SendMessage type: "shutdown_request", recipient: "explorer-1", content: "Analysis complete"
   SendMessage type: "shutdown_request", recipient: "explorer-2", content: "Analysis complete"
   [... for each explorer spawned]
   SendMessage type: "shutdown_request", recipient: "synthesizer", content: "Analysis complete"
   

5. Archive session and cleanup team:

   • If ENABLE_CHECKPOINTING = true: Move .claude/sessions/__da_live__/ to .claude/sessions/da-{timestamp}/
   • Use TeamDelete to remove the team and its task list

Error Handling

Settings Check Failure

• If .claude/agent-alchemy.local.md exists but is malformed or the deep-analysis section is unparseable: warn the user ("Settings file found but could not parse deep-analysis settings — using defaults") and proceed with default approval values.

Planning Phase Failure

• If reconnaissance fails (errors, empty results, unusual structure): fall back to static focus area templates (Step 3b)
• If the codebase appears empty: inform the user and ask how to proceed

Approval Phase Failure

• If maximum modification cycles (3) or regeneration cycles (2) are reached without approval: use AskUserQuestion with options:
  • "Approve current plan" — Proceed with the latest version of the plan
  • "Abort analysis" — Cancel the analysis entirely

Partial Worker Failure

• If one worker fails: create a follow-up task targeting the missed focus area, assign to an idle worker, add to synthesis blockedBy
• If two workers fail: attempt follow-ups, but if they also fail, instruct the synthesizer to work with partial results
• If all workers fail: inform the user and offer to retry or abort

Synthesizer Failure

• If the synthesizer fails: present the raw exploration results to the user directly
• Offer to retry synthesis or let the user work with partial results

General Failures

If any phase fails:

1. Explain what went wrong
2. Ask the user how to proceed:
   • Retry the phase
   • Continue with partial results
   • Abort the analysis

Session Recovery

When resuming from an interrupted session (detected in Phase 0 Step 2), use the following per-phase strategy:

Recovery procedure:

1. Read checkpoint.md to determine last_completed_phase and session state (team_name, explorer_names, task_ids)
2. Load any persisted artifacts from the session directory (team_plan, explorer findings, synthesis)
3. Resume from Phase last_completed_phase + 1 using the loaded state
4. For Phase 4 recovery: compare persisted explorer-{N}-findings.md files against expected explorer list to determine which explorers still need to run

Agent Coordination

• The lead (you) acts as the planner: performs recon, composes the team plan, handles approval, assigns work
• Workers explore independently — no cross-worker messaging (hub-and-spoke topology)
• The synthesizer can ask workers follow-up questions to resolve conflicts and fill gaps
• The synthesizer has Bash access for deep investigation (git history, dependency trees, static analysis)
• Wait for task dependencies to resolve before proceeding
• Handle agent failures gracefully — continue with partial results
• Agent count and focus area details come from the approved plan, not hardcoded values

When calling Task tool for teammates:

• Use model: "opus" for the synthesizer
• Use model: "sonnet" for workers
• Always include team_name parameter to join the team

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