Codebase Analysis Workflow

Execute a structured 3-phase codebase analysis workflow to gather insights.

Phase Overview

1. Deep Analysis — Explore and synthesize codebase findings via the deep-analysis skill
2. Reporting — Present structured analysis to the user
3. Post-Analysis Actions — Save, document, or retain analysis insights

---

Phase 1: Deep Analysis

Goal: Explore the codebase and synthesize findings.

1. Determine analysis context:

   • If arguments are provided, use them as the analysis context
   • If no arguments, set context to "general codebase understanding"

2. Check for cached results:

   • Check if

     .agents/sessions/exploration-cache/manifest.md

     exists
   • If found, read the manifest and verify:

     codebase_path

     matches the current working directory, and

     timestamp

     is within the configured cache TTL (default 24 hours)
   • If cache is valid, prompt the user to choose:
     • Use cached results (show the formatted cache date) — Read cached synthesis from

       .agents/sessions/exploration-cache/synthesis.md

       and recon from

       recon_summary.md

       . Set

       CACHE_HIT = true

       and

       CACHE_TIMESTAMP

       to the cache's timestamp. Skip step 3 and proceed directly to step 4.
     • Run fresh analysis — Remove the cache manifest file, set

       CACHE_HIT = false

       , and proceed to step 3
   • If no valid cache: set

     CACHE_HIT = false

     and proceed to step 3

3. Run deep-analysis workflow:

   • Refer to the deep-analysis skill and follow its workflow
   • Pass the analysis context from step 1
   • This handles reconnaissance, team planning, approval (auto-approved when skill-invoked), team creation, parallel exploration (code-explorer agents), and synthesis (code-synthesizer agent)
   • After completion, set

     CACHE_TIMESTAMP = null

     (fresh results, no prior cache)

4. Verify results and capture metadata:

   • Ensure the synthesis covers the analysis context adequately
   • If critical gaps remain, search the codebase directly to fill them
   • Record analysis metadata for Phase 2 reporting: whether results were cached (

     CACHE_HIT

     ), cache timestamp if applicable (

     CACHE_TIMESTAMP

     ), and the number of explorer agents used (from the deep-analysis team plan, or 0 if cached)

---

Phase 2: Reporting

Goal: Present a structured analysis to the user.

1. Load diagram guidance:

   • Refer to the technical-diagrams skill for Mermaid diagram conventions
   • Use Mermaid diagrams in the Architecture Overview and Relationship Map sections

2. Present the analysis: Structure the report with these sections (see Report Template below for full details):

   • Executive Summary — Lead with the most important finding
   • Architecture Overview — How the codebase is structured
   • Tech Stack — Core technologies, frameworks, and tools detected
   • Critical Files — The 5-10 most important files with details
   • Patterns & Conventions — Recurring patterns and coding conventions
   • Relationship Map — How components connect to each other
   • Challenges & Risks — Technical risks and complexity hotspots
   • Recommendations — Actionable next steps, each citing the challenge it addresses
   • Analysis Methodology — Agents used, cache status, scope, and duration

3. Proceed immediately to Phase 3.

---

Phase 3: Post-Analysis Actions

Goal: Let the user save, document, or retain analysis insights from the report through a multi-step interactive flow.

Step 1: Select actions

Prompt the user to choose (multi-select) from all available actions:

• Save Codebase Analysis Report — Write the structured report to a markdown file
• Save a custom report — Generate a report tailored to your specific goals (you'll provide instructions next)
• Update project documentation — Add/update README.md, CLAUDE.md, or AGENTS.md with analysis insights
• Keep a condensed summary in memory — Retain a quick-reference summary in conversation context

If the user selects no actions, the workflow is complete. Thank the user and end.

Step 2: Execute selected actions

Process selected actions in the following fixed order. Complete all sub-steps for each action before moving to the next.

Action: Save Codebase Analysis Report

Step 2a-1: Prompt for file location

• Check if an

  internal/docs/

  directory exists in the project root
  • If yes, suggest default path:

    internal/docs/codebase-analysis-report-{YYYY-MM-DD}.md

  • If no, suggest default path:

    codebase-analysis-report-{YYYY-MM-DD}.md

    in the project root
• Prompt the user to confirm or customize the file path

Step 2a-2: Generate and save the report

• Generate the full structured report using the Phase 2 analysis findings and the report template structure
• Write the report to the confirmed path
• Confirm the file was saved

Action: Save Custom Report

Step 2b-1: Gather report requirements

• Prompt the user to describe the goals and requirements for their custom report — what it should focus on, what questions it should answer, and any format preferences

Step 2b-2: Prompt for file location

• Check if an

  internal/docs/

  directory exists in the project root
  • If yes, suggest default path:

    internal/docs/custom-report-{YYYY-MM-DD}.md

  • If no, suggest default path:

    custom-report-{YYYY-MM-DD}.md

    in the project root
• Prompt the user to confirm or customize the file path

Step 2b-3: Generate and save the custom report

• Generate a report shaped by the user's requirements from Step 2b-1, drawing from the Phase 2 analysis data — this is a repackaging of existing findings, not a re-analysis
• Write the report to the confirmed path
• Confirm the file was saved

Action: Update Project Documentation

Step 2c-1: Select documentation files and gather directions

Prompt the user to choose (multi-select):

• README.md — Add architecture, structure, and tech stack information
• CLAUDE.md — Add patterns, conventions, critical files, and architectural decisions
• AGENTS.md — Add agent descriptions, capabilities, and coordination patterns

Then prompt for update directions for all selected files: "What content from the analysis should be added or updated? Provide general directions or specific sections to focus on (applies across all selected files, or specify per-file directions)."

Step 2c-2: Generate and approve documentation drafts

For each selected file, read the existing file and generate a draft based on the user's directions and Phase 2 analysis data:

• README.md: Read existing file at project root. If no README.md exists, skip and inform the user. Draft updates focusing on architecture, project structure, and tech stack.
• CLAUDE.md: Read existing file at project root. If none exists, ask if one should be created (if declined, skip). Draft updates focusing on patterns, conventions, critical files, and architectural decisions.
• AGENTS.md: Read existing file at project root (create new if none exists). Draft content focusing on agent inventory (name, model, purpose), capabilities and tool access, coordination patterns, skill-agent mappings, and model tiering rationale.

Present all drafts together in a single output, clearly labeled by file. Then prompt the user to choose:

• Apply all — Apply all drafted updates
• Modify — Specify which file(s) to revise and what to change (max 3 revision cycles, then must Apply or Skip)
• Skip all — Skip all documentation updates

If approved, apply updates by modifying existing files or writing new files.

Action: Keep Insights in Memory

• Present a condensed Codebase Quick Reference inline in the conversation:
  • Architecture — 1-2 sentence summary of how the codebase is structured
  • Key Files — 3-5 most critical files with one-line descriptions
  • Conventions — Important patterns and naming conventions
  • Tech Stack — Core technologies and frameworks
  • Watch Out For — Top risks or complexity hotspots
• No file is written — this summary stays in conversation context for reference during the session

Step 3: Actionable Insights Follow-up

This step always executes after Step 2 completes. The Phase 2 analysis is available in conversation context regardless of whether a report file was saved.

Prompt the user to choose:

• Address actionable insights — Fix challenges and implement recommendations from the report
• Skip — No further action needed

If the user selects "Skip", proceed to Step 4.

If the user selects "Address actionable insights":

Step 3a: Extract actionable items from the report

Parse the Phase 2 report (in conversation context) to extract items from:

• Challenges & Risks table rows — title from Challenge column, severity from Severity column, description from Impact column
• Recommendations section — each numbered item with an (addresses: {Challenge name}) citation; inherit the cited challenge's severity (High/Medium/Low). If no citation is present, default to Medium.
• Other findings with concrete fixes — default to Low severity

If no actionable items are found, inform the user and skip to Step 4.

Step 3b: Present severity-ranked item list

Present items sorted High to Medium to Low using the Actionable Insights format (see below), each showing:

• Title
• Severity (High / Medium / Low)
• Source section (Challenges & Risks, Recommendations, or Other)
• Brief description

Prompt the user to choose which items to address (multi-select). If no items selected, skip to Step 4.

Step 3c: Process each selected item in priority order (High to Medium to Low)

For each item:

1. Assess complexity:

   • Simple — Single file, clear fix, localized change
   • Complex — Multi-file, architectural impact, requires investigation

2. Plan the fix:

   • Simple: Read the target file, propose changes directly
   • Complex (architectural): Delegate to an architect agent (see

     agents/code-architect.md

     for instructions) with context: the item title, severity, description, the relevant report section text, and any files or components mentioned. The agent designs the fix and returns a proposal.
   • Complex (needs investigation): This step uses the code-explorer agent from the deep-analysis skill (see

     ../deep-analysis/agents/code-explorer.md

     ) with context: the item title, description, suspected files/components, and what needs investigation. The agent explores and returns findings for you to formulate a fix proposal.
   • If an agent delegation fails, fall back to direct investigation using file reading and searching, and propose a simpler fix based on available information.

3. Present proposal: Show files to modify, specific changes, and rationale

4. User approval — Prompt the user to choose:

   • Apply — Execute changes, confirm success
   • Skip — Record the skip, move to next item
   • Modify — User describes adjustments, re-propose the fix (max 3 revision cycles, then must Apply or Skip)

Step 3d: Summarize results

Present a summary covering:

• Items addressed (with list of files modified per item)
• Items skipped
• Total files modified table

Step 4: Complete the workflow

Summarize which actions were executed and confirm the workflow is complete.

---

Error Handling

General

If any phase fails:

1. Explain what went wrong
2. Ask the user how to proceed:
   • Retry the phase
   • Skip to next phase (with partial results)
   • Abort the workflow

Documentation Update Failures (Step 2c)

If a file write or edit fails when applying documentation updates:

1. Retry the operation once
2. If still failing, present the drafted content to the user inline and suggest they apply it manually
3. Continue with the remaining selected files

Agent Delegation Failures (Step 3c)

If a code-architect or code-explorer agent fails during actionable insight processing:

1. Fall back to direct investigation using file reading and searching
2. Propose a simpler fix based on available information
3. If the item is too complex to address without agent assistance, inform the user and offer to skip

---

Agent Coordination

Exploration and synthesis agent coordination is handled by the deep-analysis skill in Phase 1, which uses agent teams with hub-and-spoke coordination. Deep-analysis performs reconnaissance, composes a team plan (auto-approved when invoked by another skill), assembles the team, and manages the exploration/synthesis lifecycle. See that skill for team setup, approval flow, and failure handling details.

---

Nested Agents

This skill uses the following nested agent:

• agents/code-architect.md

  — Designs implementation blueprints for fixing complex architectural issues identified in the analysis report.

This skill also cross-references agents from the deep-analysis skill:

• ../deep-analysis/agents/code-explorer.md

  — Used in Step 3c for investigating complex items that need codebase exploration before a fix can be proposed.

---

Report Template

Use this template when presenting analysis findings in Phase 2.

# Codebase Analysis Report

**Analysis Context**: {What was analyzed and why}
**Codebase Path**: {Path analyzed}
**Date**: {YYYY-MM-DD}

{If the report exceeds approximately 100 lines, add a **Table of Contents** here linking to each major section.}

---

## Executive Summary

{Lead with the most important finding. 2-3 sentences covering: what was analyzed, the key architectural insight, and the primary recommendation or risk.}

---

## Architecture Overview

{2-3 paragraphs describing:}
- How the codebase is structured (layers, modules, boundaries)
- The design philosophy and architectural style
- Key architectural decisions and their rationale

{Include a Mermaid architecture diagram (flowchart or C4 Context) showing the major layers/components. Use `classDef` with `color:#000` for all node styles.}

---

## Tech Stack

| Category | Technology | Version (if detected) | Role |
|----------|-----------|----------------------|------|
| Language | {e.g., TypeScript} | {e.g., 5.x} | Primary language |
| Framework | {e.g., Next.js} | {e.g., 16} | Web framework |

{Include only technologies actually detected in config files or code. Omit categories that don't apply.}

---

## Critical Files

{Limit to 5-10 most important files}

| File | Purpose | Relevance |
|------|---------|-----------|
| `path/to/file` | Brief description | High/Medium |

### File Details

#### `path/to/critical-file`
- **Key exports**: What this file provides to others
- **Core logic**: What it does
- **Connections**: What depends on it and what it depends on

---

## Patterns & Conventions

### Code Patterns
- **Pattern**: Description and where it's used

### Naming Conventions
- **Convention**: Description and examples

### Project Structure
- **Organization**: How files and directories are organized

---

## Relationship Map

{Describe how key components connect — limit to 15-20 most significant connections. Use Mermaid flowcharts for both data flows and dependency maps.}

---

## Challenges & Risks

| Challenge | Severity | Impact |
|-----------|----------|--------|
| {Description} | High/Medium/Low | {What could go wrong} |

---

## Recommendations

1. **{Recommendation}** _(addresses: {Challenge name})_: {Brief rationale}
2. **{Recommendation}** _(addresses: {Challenge name})_: {Brief rationale}

---

## Analysis Methodology

- **Exploration agents**: {Number} agents with focus areas: {list}
- **Synthesis**: Findings merged and critical files read in depth
- **Scope**: {What was included and what was intentionally excluded}
- **Cache status**: {Fresh analysis / Cached results from YYYY-MM-DD}

Report Section Guidelines

Executive Summary: Lead with the most important finding, not a generic overview. Keep to 2-3 sentences. Include at least one actionable insight.

Critical Files: Limit to 5-10 files that someone must understand. Include both the "what" (purpose) and "why" (relevance to analysis context).

Patterns & Conventions: Only include patterns that are consistently applied. Note deviations from patterns — these are often more interesting than the patterns themselves.

Relationship Map: Focus on the most important connections, not an exhaustive dependency graph. Use directional language (calls, depends on, triggers, reads from). Cap at 15-20 connections.

Challenges & Risks: Rate severity based on likelihood and impact combined. Include specific details, not vague warnings.

Recommendations: Make recommendations actionable. Each must reference the specific challenge it addresses using the format: (addresses: {Challenge name}). Limit to 3-5 recommendations.

Adapting the Template

For Feature-Focused Analysis: Emphasize integration points and files that would need modification. Include a "Feature Implementation Context" section before Recommendations.

For General Codebase Understanding: Broader Architecture Overview with layer descriptions. More extensive Patterns & Conventions section.

For Debugging/Investigation: Emphasize the execution path and data flow. Include a "Relevant Execution Paths" section.

---

Actionable Insights Format

Item List Format

Present extracted items grouped by severity, highest first:

### High Severity

1. **{Title}** — _{Source: Challenges & Risks}_
   {Brief description of the issue and its impact}

### Medium Severity

2. **{Title}** — _{Source: Recommendations}_
   {Brief description and rationale}

### Low Severity

3. **{Title}** — _{Source: Other Findings}_
   {Brief description}

Severity Assignment Guidelines

From Challenges & Risks Table: Use the Severity column value directly. Title comes from the Challenge column. Description comes from the Impact column.

From Recommendations Section: Each recommendation should cite which challenge it addresses. Use this citation to inherit severity. If no challenge link is present, default to Medium.

From Other Findings: Default to Low unless the finding explicitly describes a critical issue.

Complexity Assessment Criteria

Complexity	Typical Effort	Description
Simple	Low (~minutes)	Single targeted change, clear fix
Complex — Architectural	Medium-High (~30min-1hr+)	Multi-file refactoring, design decisions
Complex — Investigation	Medium (~15-30min) + varies	Investigation phase + fix implementation

Change Proposal Format

#### {Item Title} ({Severity})

**Complexity:** Simple / Complex (architectural) / Complex (investigation)
**Effort:** Low (~minutes) / Medium (~30min) / High (~1hr+)

**Files to modify:**
| File | Change Type |
|------|-------------|
| `path/to/file` | Edit / Create / Delete |

**Proposed changes:**
{Description of what will change and why.}

**Rationale:**
{Why this approach was chosen. Reference the original finding.}

Summary Format

## Actionable Insights Summary

### Items Addressed
| # | Item | Severity | Files Modified |
|---|------|----------|----------------|
| 1 | {Title} | High | `file1.ts`, `file2.ts` |

### Items Skipped
| # | Item | Severity | Reason |
|---|------|----------|--------|
| 2 | {Title} | Low | User skipped |

### Files Modified
| File | Changes |
|------|---------|
| `path/to/file` | {Brief description of change} |

**Total:** {N} items addressed, {M} items skipped, {P} files modified

Processing Guidelines

• Only extract items with concrete, actionable fixes — skip vague observations
• Deduplicate items that target the same file/component or have significant keyword overlap
• Process items in the order the user selected them, but within that, prioritize by severity
• Before starting fixes, scan for potential conflicts (same-file modifications, contradictory changes, ordering dependencies). If conflicts are detected, present them to the user before proceeding.
• Maximum 3 revision cycles per item when user selects "Modify"