Deep Analysis

Deep Analysis Workflow

Execute a structured exploration + synthesis workflow using 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 deep investigation.

This skill can be invoked standalone or loaded by other skills as a reusable building block. Approval behavior is configurable.

Settings Check

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

1. Read settings:

   • Check configuration for deep-analysis settings
   • Look for a deep-analysis section with nested settings:
     • direct-invocation-approval: Whether to require plan approval when invoked directly (default: true)
     • invocation-by-skill-approval: Whether to require approval when loaded by another skill (default: false)

2. Determine invocation mode:

   • Direct invocation: The user invoked this skill directly, or it is running 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 settings are missing, use defaults
   • If the settings are 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):

   • 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 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 .agents/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: Prompt the user to choose:
     • 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 .agents/sessions/__da_live__/checkpoint.md exists
2. If found, read the checkpoint to determine last_completed_phase
3. Prompt the user to choose:
   • 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 .agents/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 .agents/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.

1. Determine analysis context:

   • Accept the following inputs: an analysis context or focus area
   • If no inputs and this skill was loaded by another skill, use the calling skill's context
   • If no inputs 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: Quickly map the codebase structure. This should take 1-2 minutes, not deep investigation.

   • Directory structure: Search for top-level directories 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: Search 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: Search file contents 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: Patterns to find related code
   • Complexity estimate: Low/Medium/High based on file count and apparent structure

   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:** [patterns]
   - **Complexity:** [Low/Medium/High]
   - **Assigned to:** explorer-1
   
   #### Focus Area 2: [Label]
   - **Directories:** [list]
   - **Starting files:** [2-3 files]
   - **Search patterns:** [patterns]
   - **Complexity:** [Low/Medium/High]
   - **Assigned to:** explorer-2
   
   [... repeated for each focus area]
   
   ### Worker Composition
   | Role | Count | Purpose |
   |------|-------|---------|
   | Explorer | [N] | Independent focus area exploration |
   | Synthesizer | 1 | 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 .agents/sessions/__da_live__/checkpoint.md: set current_phase: 1
   • Write .agents/sessions/__da_live__/team_plan.md with the full team plan from Step 4
   • Write .agents/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 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 prompt the user to choose:

   • 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
   • Apply modifications to the team plan (adjust focus areas, worker 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
   • 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 .agents/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: Set up workers, create tasks, and assign work using the approved plan.

1. Prepare workers: Based on the approved plan, prepare the following workers:

   • N explorers (one per focus area): Refer to the code-explorer skill for exploration behavior. Each explorer investigates their assigned focus area independently.
   • 1 synthesizer: Refer to the code-synthesizer skill for synthesis behavior. The synthesizer has shell access for git history, dependency analysis, and static analysis.

2. Create tasks: For each focus area, create an exploration task with: subject ("Explore: [Focus area label]"), detailed exploration instructions including directories, starting files, search terms, and complexity estimate.

   Create a synthesis task: "Synthesize and evaluate exploration findings" -- blocked by all exploration tasks.

3. Assign exploration tasks: For each exploration task, delegate to the corresponding explorer worker with the task details: focus area label, directories, starting files, and search patterns.

4. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .agents/sessions/__da_live__/checkpoint.md: set current_phase: 3, record worker names, task assignments
   • Append to progress.md: [timestamp] Phase 3: Team assembled -- [N] explorers, 1 synthesizer

Phase 4: Focused Exploration

Goal: Workers explore their assigned areas independently.

Monitoring

After assigning exploration tasks, monitor progress:

1. When an explorer completes, record their findings. If ENABLE_CHECKPOINTING = true, write explorer-{N}-findings.md to .agents/sessions/__da_live__/ and update checkpoint.
2. Workers explore independently -- no cross-worker communication (hub-and-spoke topology)
3. Workers can respond to follow-up questions from the synthesizer
4. Each worker marks its task as completed when done
5. Wait for all exploration tasks to complete before proceeding to Phase 5

Phase 5: Evaluation and Synthesis

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

Step 1: Structural Completeness Check

This is a structural check, not a quality assessment:

1. Verify all exploration tasks are completed
2. Check that each worker produced a report with content
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
   • Wait for the follow-up to complete
4. If all produced content: proceed immediately to Step 2

Step 2: Launch Synthesis

1. Assign the synthesis task to the synthesizer worker

2. Provide the synthesizer with:

   • Analysis context and codebase path
   • Reconnaissance findings from Phase 1
   • The list of explorer workers (for follow-up questions if needed)
   • Instructions to read exploration task results, synthesize into a unified analysis, and evaluate completeness before finalizing

3. The synthesizer has shell access for deep investigation -- git history analysis, dependency trees, static analysis, or any investigation that basic file reading cannot handle

4. Wait for the synthesizer to complete

5. Checkpoint (if ENABLE_CHECKPOINTING = true):

   • Update .agents/sessions/__da_live__/checkpoint.md: set current_phase: 5
   • Write .agents/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 clean up.

1. Collect synthesis output:

   • Read the synthesis results from the synthesizer

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

   • Create .agents/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. Shut down workers: Signal all workers that analysis is complete and they can stop.

5. Archive session and cleanup:

   • If ENABLE_CHECKPOINTING = true: Move .agents/sessions/__da_live__/ to .agents/sessions/da-{timestamp}/
   • Clean up any temporary team/task resources

Error Handling

Settings Check Failure

• If settings exist but are malformed or unparseable: warn the user ("Settings 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, prompt the user to choose:
  • 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
• 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 (worker names, task assignments)
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

Coordination

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

Integration Notes

What this component does: Orchestrates a multi-phase deep analysis workflow: reconnaissance, dynamic planning, user approval, parallel exploration via independent workers, synthesis with deep investigation, caching, and session checkpointing/recovery.

Origin: Skill (orchestrator, keystone)

Capabilities needed:

• File reading, writing, and search (for reconnaissance, caching, checkpointing)
• Shell command execution (for the synthesizer's deep investigation: git history, dependency trees, static analysis)
• User interaction/prompting (for approval flow, cache decisions, session recovery)
• Task/worker delegation (for spawning explorer and synthesizer workers)
• Background task monitoring (for tracking explorer completion)

Adaptation guidance:

• The hub-and-spoke coordination pattern originally used platform-specific TeamCreate/TaskCreate/SendMessage/TaskUpdate APIs. Adapt to whatever task delegation and messaging mechanism the target harness provides.
• Explorer workers were originally spawned as Sonnet-tier agents; the synthesizer as Opus-tier. If the target harness supports model selection, preserve this tiering for cost efficiency.
• Session checkpointing writes to .agents/sessions/__da_live__/. If the target harness has its own session/state management, adapt accordingly.
• The approval flow uses interactive prompts. If the target harness is non-interactive, default to auto-approval.