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 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 file:
2. Check if a configuration file exists for the project
3. If it exists, look for a deep-analysis section with these settings:
4. direct-invocation-approval: Whether to require approval when invoked directly (default: true)
5. invocation-by-skill-approval: Whether to require approval when loaded by another skill (default: false)
6. cache-ttl-hours: Hours before exploration cache expires; 0 disables caching (default: 24)
7. enable-checkpointing: Write session checkpoints at phase boundaries (default: true)
8. enable-progress-indicators: Display phase progress messages (default: true)

1. Determine invocation mode:
2. Direct invocation: The user invoked deep-analysis directly or standalone
3. Skill-invoked: Another skill (e.g., codebase-analysis, feature-dev, docs-manager) loaded and is executing this workflow

1. Resolve settings:
2. Use found settings, or defaults if absent
3. If the file is malformed, warn the user and use defaults

1. Set behavioral flags:
2. REQUIRE_APPROVAL = direct-invocation-approval (if direct) or invocation-by-skill-approval (if skill-invoked)
3. CACHE_TTL = cache-ttl-hours value
4. ENABLE_CHECKPOINTING = enable-checkpointing value
5. ENABLE_PROGRESS = enable-progress-indicators value

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:
3. analysis_context matches the current analysis context (or is a superset)
4. codebase_path matches the current working directory
5. timestamp is within CACHE_TTL hours of now
6. Config files referenced in config_checksum have not been modified since the cache was written (check mod-times of package.json, tsconfig.json, pyproject.toml, etc.)
7. If cache is valid:
8. 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).
9. Direct invocation: Prompt the user to choose:
10. Use cached results — Set CACHE_HIT = true, skip to Phase 6 step 2
11. Refresh analysis — Set CACHE_HIT = false, proceed normally
12. 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:
4. Resume from Phase [N+1] — Load checkpoint state, proceed from the interrupted phase (see Session Recovery in Error Handling)
5. Start fresh — Archive the interrupted session to .agents/sessions/da-interrupted-{timestamp}/ and proceed normally
6. 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:

```markdown ## Deep Analysis Session

• analysis_context: [context from arguments or caller]
• codebase_path: [current working directory]
• started: [ISO timestamp]
• current_phase: 0
• status: initialized

```

1. Write progress.md:

```markdown ## 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:
2. If arguments are provided, use them as the analysis context (feature area, question, or general exploration goal)
3. If no arguments and this skill was loaded by another skill, use the calling skill's context
4. If no arguments and standalone invocation, set context to "general codebase understanding"
5. Set PATH = current working directory
6. Inform the user: "Exploring codebase at: PATH" with the analysis context

1. Rapid codebase reconnaissance:

Quickly map the codebase structure. This should take 1-2 minutes, not deep investigation.

• Directory structure: List 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 for files 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 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.

1. 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

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 con