<quick_start> Basic usage:

/apex add authentication middleware

Recommended workflow (autonomous with save):

/apex -a -s implement user registration

With adversarial review:

/apex -a -x -s fix login bug

Flags:

• -a (auto): Skip confirmations
• -s (save): Save outputs to .claude/output/apex/
• -x (examine): Include adversarial code review
• -t (test): Create and run tests
• -pr (pull-request): Create PR at end

See <parameters> for complete flag list. </quick_start>

Disable flags (turn OFF):

Autonomous mode (no confirmations)

/apex -a add auth middleware

Save outputs for review

/apex -s add auth middleware

With adversarial review

/apex -x add auth middleware

Full autonomous with examine and save

/apex -a -x -s add auth middleware

Include test creation and runner

/apex -t add auth middleware

Resume a previous task

/apex -r 01-auth-middleware /apex -r 01 # Partial match supported

Combined flags

/apex -a -x -s -t add auth middleware

Branch mode (ensure not on main, create branch if needed)

/apex -b add auth middleware

Create PR at end (automatically enables -b)

/apex -pr add auth middleware /apex -a -pr add auth middleware # Auto + PR mode

Interactive mode (configure flags via menu)

/apex -i add auth middleware

Economy mode (save tokens, no subagents)

/apex -e add auth middleware /apex -a -e add auth middleware # Auto + economy

Disable flags (override defaults)

/apex -A add auth middleware # Disable auto (if default is true) /apex -S -T add auth middleware # Disable save and test /apex --no-auto add auth middleware

</examples>

<parsing_rules>
**Flag parsing:**

1. Defaults loaded from `steps/step-00-init.md` `<defaults>` section
2. Command-line flags override defaults (enable with lowercase `-x`, disable with uppercase `-X`)
3. Flags removed from input, remainder becomes `{task_description}`
4. Task ID generated as `NN-kebab-case-description`

For detailed parsing algorithm, see `steps/step-00-init.md`.
</parsing_rules>

</parameters>

<output_structure>
**When `{save_mode}` = true:**

All outputs saved to PROJECT directory (where Claude Code is running):

.claude/output/apex/{task-id}/ ├── 00-context.md # Params, user request, timestamp ├── 01-analyze.md # Analysis findings ├── 02-plan.md # Implementation plan ├── 03-execute.md # Execution log ├── 04-validate.md # Validation results ├── 05-examine.md # Review findings (if -x) ├── 06-resolve.md # Resolution log (if -x) ├── 07-tests.md # Test analysis and creation (if --test) ├── 08-run-tests.md # Test runner log (if --test) └── 09-finish.md # Workflow finish and PR creation (if --pull-request)

**00-context.md structure:**
```markdown
# APEX Task: {task_id}

**Created:** {timestamp}
**Task:** {task_description}

## Flags
- Auto mode: {auto_mode}
- Examine mode: {examine_mode}
- Save mode: {save_mode}
- Test mode: {test_mode}

## User Request
{original user input}

## Acceptance Criteria
- [ ] AC1: {inferred criterion}
- [ ] AC2: {inferred criterion}

</output_structure>

<resume_workflow> Resume mode (-r {task-id}):

When provided, step-00 will:

1. Locate the task folder in .claude/output/apex/
2. Restore state from 00-context.md
3. Find the last completed step
4. Continue from the next step

Supports partial matching (e.g., -r 01 finds 01-add-auth-middleware).

For implementation details, see steps/step-00-init.md. </resume_workflow>

<state_variables> Persist throughout all steps:

</state_variables>

<entry_point>

FIRST ACTION: Load steps/step-00-init.md

Step 00 handles:

• Flag parsing (-a, -x, -s, -r, --test)
• Resume mode detection and task lookup
• Output folder creation (if save_mode)
• 00-context.md creation (if save_mode)
• State variable initialization

After initialization, step-00 loads step-01-analyze.md.

</entry_point>

<step_files> Progressive loading - only load current step:

</step_files>

<execution_rules>

• Load one step at a time - Only load the current step file
• ULTRA THINK before major decisions
• Persist state variables across all steps
• Follow next_step directive at end of each step
• Save outputs if {save_mode} = true (append to step file)
• Use parallel agents for independent exploration tasks </execution_rules>

<save_output_pattern> When {save_mode} = true:

Step-00 runs scripts/setup-templates.sh to initialize all output files from templates/ directory.

Each step then:

1. Run scripts/update-progress.sh {task_id} {step_num} {step_name} "in_progress"
2. Append findings/outputs to the pre-created step file
3. Run scripts/update-progress.sh {task_id} {step_num} {step_name} "complete"

Template system benefits:

• Reduces token usage by ~75% (1,350 tokens saved per workflow)
• Templates in templates/ directory (not inline in steps)
• Scripts handle progress tracking automatically
• See templates/README.md for details

</save_output_pattern>

<success_criteria>

• Each step loaded progressively
• All validation checks passing
• Outputs saved if {save_mode} enabled
• Tests passing if {test_mode} enabled
• Clear completion summary provided </success_criteria>