Codebase Analysis Workflow

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

CRITICAL: Complete ALL 3 phases. The workflow is not complete until Phase 3: Post-Analysis Actions is finished. After completing each phase, immediately proceed to the next phase without waiting for user prompts.

Phase Overview

1. Deep Analysis — Explore and synthesize codebase findings via 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

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

2. Check for cached results:

   • Check if

     .claude/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, use

     AskUserQuestion

     :
     • Use cached results (show the formatted cache date) — Read cached synthesis from

       .claude/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:

   • Read

     ${CLAUDE_PLUGIN_ROOT}/skills/deep-analysis/SKILL.md

     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, use Glob/Grep to fill them directly
   • 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:

   • Read

     ${CLAUDE_PLUGIN_ROOT}/skills/technical-diagrams/SKILL.md

   • Use Mermaid diagrams in the Architecture Overview and Relationship Map sections

2. Load report template:

   • Read

     ${CLAUDE_PLUGIN_ROOT}/skills/codebase-analysis/references/report-template.md

   • Use it to structure the presentation

3. Present the analysis: Structure the report with these sections:

   • 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

4. IMPORTANT: Proceed immediately to Phase 3. Do NOT stop here. Do NOT wait for user input. The report is presented, but the workflow requires Post-Analysis Actions. Continue directly to Phase 3 now.

---

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

Use

AskUserQuestion

with

multiSelect: true

to present 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
• Use

  AskUserQuestion

  to let the user confirm or customize the file path

Step 2a-2: Generate and save the report

• Use the report template already loaded in Phase 2 Step 1
• Generate the full structured report using the Phase 2 analysis findings and the template structure
• Write the report to the confirmed path using the Write tool
• Confirm the file was saved

Action: Save Custom Report

Step 2b-1: Gather report requirements

• Use

  AskUserQuestion

  to ask 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
• Use

  AskUserQuestion

  to let the user 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 using the Write tool
• Confirm the file was saved

Action: Update Project Documentation

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

Use

AskUserQuestion

with

multiSelect: true

:

• 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 use a single

AskUserQuestion

to gather 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 use

AskUserQuestion

:

• 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 using Edit tool (existing files) or Write tool (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

Condition: 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.

Use

AskUserQuestion

to ask:

• 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

• Load reference template from

  ${CLAUDE_PLUGIN_ROOT}/skills/codebase-analysis/references/actionable-insights-template.md

• Present items sorted High → Medium → Low, each showing:
  • Title
  • Severity (High / Medium / Low)
  • Source section (Challenges & Risks, Recommendations, or Other)
  • Brief description
• Use

  AskUserQuestion

  with

  multiSelect: true

  for the user to select which items to address
• If no items selected, skip to Step 4

Step 3c: Process each selected item in priority order (High → Medium → 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): Launch

     agent-alchemy-core-tools:code-architect

     agent with context: the item title, severity, description, the relevant report section text (copy the specific Challenges/Recommendations entry), and any files or components mentioned. The agent designs the fix and returns a proposal.
   • Complex (needs investigation): Launch

     agent-alchemy-core-tools:code-explorer

     agent 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 launch fails, fall back to direct investigation using Read/Glob/Grep and propose a simpler fix based on available information.

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

4. User approval via

   AskUserQuestion

   :
   • Apply — Execute changes with Edit/Write tools, 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 an Edit or Write call 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 Launch Failures (Step 3c)

If a

code-architect

or

code-explorer

agent fails during actionable insight processing:

1. Fall back to direct investigation using Read, Glob, and Grep
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, agent model tiers, and failure handling details.

---

Additional Resources

• For report structure, see references/report-template.md
• For actionable insights format, see references/actionable-insights-template.md