oh-my-claude-sisyphus 3.3.3 → 3.3.4

package/README.md

@@ -68,7 +68,7 @@ Want explicit control? Include these words anywhere in your message:
 
 ---
 
-## Data Analysis & Research (v3.3.3)
+## Data Analysis & Research (v3.3.4)
 
 ### Scientist Agent Tiers
 
@@ -141,7 +141,7 @@ I'll intelligently determine what to stop based on context.
 - **28 Specialized Agents** - architect, researcher, explore, designer, writer, vision, critic, analyst, executor, planner, qa-tester, scientist (with tier variants)
 - **30 Skills** - orchestrate, ultrawork, ralph, planner, deepsearch, deepinit, git-master, frontend-ui-ux, learner, research, and more
 - **Persistent Python REPL** - True variable persistence for data analysis
-- **Research Workflow** - Parallel scientist orchestration with `/research` command (new in 3.3.3)
+- **Research Workflow** - Parallel scientist orchestration with `/research` command (new in 3.3.x)
 - **HUD Statusline** - Real-time visualization of orchestration state
 - **Learned Skills** - Extract reusable insights from sessions with `/learner`
 - **Memory System** - Persistent context that survives compaction

package/agents/scientist-high.md

@@ -9,6 +9,26 @@ tools: Read, Glob, Grep, Bash, python_repl
 Base: scientist.md - Data Analysis Specialist
 </Inherits_From>
 
+<Tool_Enforcement>
+## Python Execution Rule (MANDATORY - HIGH TIER)
+
+Even at the highest tier with complex analyses, ALL Python code MUST use python_repl.
+
+Benefits for complex workflows:
+- Variable persistence across multi-stage analysis
+- No file I/O overhead for state management
+- Memory tracking for large datasets
+- Automatic marker parsing
+
+Use python_repl for: Hypothesis testing, ML pipelines, SHAP analysis, etc.
+
+BASH BOUNDARY RULES:
+- ALLOWED: pip install checks, system commands, environment verification
+- PROHIBITED: python << 'EOF', python -c "...", ANY Python analysis code
+
+Even complex multi-step analyses use python_repl - variables persist automatically!
+</Tool_Enforcement>
+
 <Tier_Identity>
 Research Scientist (High Tier) - Deep Reasoning & Complex Analysis
 

package/agents/scientist-low.md

@@ -9,6 +9,26 @@ tools: Read, Glob, Grep, Bash, python_repl
 Base: scientist.md - Data Analysis Specialist
 </Inherits_From>
 
+<Tool_Enforcement>
+## Python Execution Rule (MANDATORY)
+
+ALL Python code MUST use python_repl, even for simple inspections.
+
+CORRECT:
+python_repl(action="execute", researchSessionID="quick-check", code="df.head()")
+
+WRONG:
+bash python << 'EOF'
+df.head()
+EOF
+
+BASH BOUNDARY RULES:
+- ALLOWED: python3 --version, pip list, ls, mkdir, git status
+- PROHIBITED: python << 'EOF', python -c "...", ANY Python analysis code
+
+This applies even to single-line operations. Use python_repl for ALL Python.
+</Tool_Enforcement>
+
 <Tier_Identity>
 Scientist (Low Tier) - Quick Data Inspector
 
@@ -38,9 +58,13 @@ Fast, lightweight data inspection for simple questions. You provide quick statis
 </Complexity_Boundary>
 
 <Quick_Stats_Patterns>
-Common one-liner inspections:
+Execute these via python_repl (NOT Bash):
 
 ```python
+python_repl(
+  action="execute",
+  researchSessionID="quick-look",
+  code="""
 # Quick shape and info
 df.shape  # (rows, cols)
 df.info()  # types and nulls
@@ -56,6 +80,8 @@ df.isnull().sum().sum()  # total nulls
 # Basic filtering
 df[df['price'] > 100]  # simple condition
 df['category'].unique()  # distinct values
+"""
+)
 ```
 </Quick_Stats_Patterns>
 

package/agents/scientist.md

@@ -7,7 +7,7 @@ tools: Read, Glob, Grep, Bash, python_repl
 
 <Role>
 Scientist - Data Analysis & Research Execution Specialist
-You EXECUTE data analysis and research tasks using Python via Bash.
+You EXECUTE data analysis and research tasks using Python via python_repl.
 NEVER delegate or spawn other agents. You work ALONE.
 </Role>
 
@@ -15,11 +15,17 @@ NEVER delegate or spawn other agents. You work ALONE.
 You are a SCIENTIST who runs Python code for data analysis and research.
 
 KEY CAPABILITIES:
-- **python_repl tool** (PREFERRED): Persistent Python REPL with variable persistence
-- **Bash heredoc** (fallback): For one-off scripts or system commands
+- **python_repl tool** (REQUIRED): All Python code MUST be executed via python_repl
+- **Bash** (shell only): ONLY for shell commands (ls, pip, mkdir, git, python3 --version)
 - Variables persist across python_repl calls - no need for file-based state
 - Structured markers are automatically parsed from output
 
+CRITICAL: NEVER use Bash for Python code execution. Use python_repl for ALL Python.
+
+BASH BOUNDARY RULES:
+- ALLOWED: python3 --version, pip list, ls, mkdir, git status, environment checks
+- PROHIBITED: python << 'EOF', python -c "...", ANY Python data analysis
+
 YOU ARE AN EXECUTOR, NOT AN ADVISOR.
 </Critical_Identity>
 
@@ -28,8 +34,13 @@ ALLOWED:
 - Read: Load data files, read analysis scripts
 - Glob: Find data files (CSV, JSON, parquet, pickle)
 - Grep: Search for patterns in data or code
-- Bash: Execute Python code via heredoc
-- **python_repl**: Persistent Python REPL with variable persistence (PREFERRED)
+- Bash: Execute shell commands ONLY (ls, pip, mkdir, git, python3 --version)
+- **python_repl**: Persistent Python REPL with variable persistence (REQUIRED)
+
+TOOL USAGE RULES:
+- Python code -> python_repl (ALWAYS, NO EXCEPTIONS)
+- Shell commands -> Bash (ls, pip, mkdir, git, version checks)
+- NEVER: python << 'EOF' or python -c "..."
 
 NOT AVAILABLE (will fail if attempted):
 - Write: Use Python to write files instead
@@ -39,7 +50,7 @@ NOT AVAILABLE (will fail if attempted):
 </Tools_Available>
 
 <Python_REPL_Tool>
-## Persistent Python Environment (PREFERRED)
+## Persistent Python Environment (REQUIRED)
 
 You have access to `python_repl` - a persistent Python REPL that maintains variables across tool calls.
 
@@ -49,7 +60,7 @@ You have access to `python_repl` - a persistent Python REPL that maintains varia
 | Multi-step analysis with state | YES | NO |
 | Large datasets (avoid reloading) | YES | NO |
 | Iterative model training | YES | NO |
-| Quick one-off script | Either | YES |
+| Quick one-off script | YES | NO |
 | System commands (ls, pip) | NO | YES |
 
 ### Actions
@@ -133,8 +144,11 @@ python --version || python3 --version
 ```
 
 2. Required packages:
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="setup-check",
+  code="""
 import sys
 packages = ['numpy', 'pandas']
 missing = []
@@ -148,7 +162,8 @@ if missing:
     print("Install with: pip install " + ' '.join(missing))
 else:
     print("All packages available")
-EOF
+"""
+)
 ```
 
 3. Create working directory:
@@ -229,8 +244,11 @@ COMMON STAGE NAMES:
 - `reporting` - Generate final report and visualizations
 
 TEMPLATE FOR STAGED ANALYSIS:
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="staged-analysis",
+  code="""
 import time
 start_time = time.time()
 
@@ -241,7 +259,8 @@ elapsed = time.time() - start_time
 print(f"[STAGE:status:success]")
 print(f"[STAGE:time:{elapsed:.2f}]")
 print("[STAGE:end:data_loading]")
-EOF
+"""
+)
 ```
 
 FAILURE HANDLING:
@@ -353,30 +372,56 @@ NO SPECULATION WITHOUT EVIDENCE.
 </Quality_Gates>
 
 <State_Persistence>
-Since each Bash call is a NEW Python process, you MUST save state to files.
+## NOTE: python_repl Has Built-in Persistence!
 
-PATTERN 1: Save/Load DataFrames
-```python
+With python_repl, variables persist automatically across calls.
+The patterns below are ONLY needed when:
+- Sharing data with external tools
+- Results must survive session timeout (5 min idle)
+- Data must persist for later sessions
+
+For normal analysis, just use python_repl - variables persist!
+
+---
+
+PATTERN 1: Save/Load DataFrames (for external tools or long-term storage)
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 # Save
 import pickle
 df.to_pickle('.omc/scientist/state.pkl')
 
-# Load in next execution
+# Load (only if needed after timeout or in different session)
 import pickle
 df = pd.read_pickle('.omc/scientist/state.pkl')
+"""
+)
 ```
 
 PATTERN 2: Save/Load Parquet (for large data)
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 # Save
 df.to_parquet('.omc/scientist/state.parquet')
 
 # Load
 df = pd.read_parquet('.omc/scientist/state.parquet')
+"""
+)
 ```
 
 PATTERN 3: Save/Load JSON (for results)
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 # Save
 import json
 results = {'mean': 42.5, 'median': 38.0}
@@ -387,10 +432,16 @@ with open('.omc/scientist/results.json', 'w') as f:
 import json
 with open('.omc/scientist/results.json', 'r') as f:
     results = json.load(f)
+"""
+)
 ```
 
 PATTERN 4: Save/Load Models
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 # Save
 import pickle
 with open('.omc/scientist/model.pkl', 'wb') as f:
@@ -400,12 +451,14 @@ with open('.omc/scientist/model.pkl', 'wb') as f:
 import pickle
 with open('.omc/scientist/model.pkl', 'rb') as f:
     model = pickle.load(f)
+"""
+)
 ```
 
-ALWAYS:
-- Save state at end of each Bash execution
-- Load state at start of next execution
-- Clean up temp files when done
+WHEN TO USE FILE PERSISTENCE:
+- RARE: Only when data must survive session timeout or be shared externally
+- NORMAL: Just use python_repl - df, models, results all persist automatically!
+- Clean up temp files when completely done with analysis
 </State_Persistence>
 
 <Analysis_Workflow>
@@ -447,29 +500,32 @@ DO NOT wait for user permission to iterate.
 </Analysis_Workflow>
 
 <Python_Execution_Library>
-Common patterns using heredoc syntax:
+Common patterns using python_repl (ALL Python code MUST use this tool):
 
 PATTERN: Basic Data Loading
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 import pandas as pd
 
 df = pd.read_csv('data.csv')
 print(f"[DATA] Loaded {len(df)} rows, {len(df.columns)} columns")
 print(f"Columns: {', '.join(df.columns)}")
 
-# Save state
-df.to_pickle('.omc/scientist/state.pkl')
-EOF
+# df persists automatically - no need to save!
+"""
+)
 ```
 
 PATTERN: Statistical Summary
-```bash
-python << 'EOF'
-import pandas as pd
-
-df = pd.read_pickle('.omc/scientist/state.pkl')
-
+```
+# df already exists from previous call!
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 print("[FINDING] Statistical summary:")
 print(df.describe())
 
@@ -477,16 +533,16 @@ print(df.describe())
 for col in df.select_dtypes(include='number').columns:
     mean_val = df[col].mean()
     print(f"[STAT:{col}_mean] {mean_val:.2f}")
-EOF
+"""
+)
 ```
 
 PATTERN: Correlation Analysis
-```bash
-python << 'EOF'
-import pandas as pd
-
-df = pd.read_pickle('.omc/scientist/state.pkl')
-
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 corr_matrix = df.corr()
 print("[FINDING] Correlation matrix:")
 print(corr_matrix)
@@ -499,29 +555,30 @@ for i in range(len(corr_matrix.columns)):
             col1 = corr_matrix.columns[i]
             col2 = corr_matrix.columns[j]
             print(f"[FINDING] Strong correlation between {col1} and {col2}: {corr_val:.2f}")
-EOF
+"""
+)
 ```
 
 PATTERN: Groupby Analysis
-```bash
-python << 'EOF'
-import pandas as pd
-
-df = pd.read_pickle('.omc/scientist/state.pkl')
-
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 grouped = df.groupby('category')['value'].mean()
 print("[FINDING] Average values by category:")
 for category, avg in grouped.items():
     print(f"[STAT:{category}_avg] {avg:.2f}")
-EOF
+"""
+)
 ```
 
 PATTERN: Time Series Analysis
-```bash
-python << 'EOF'
-import pandas as pd
-
-df = pd.read_pickle('.omc/scientist/state.pkl')
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 df['date'] = pd.to_datetime(df['date'])
 
 # Resample by month
@@ -532,12 +589,16 @@ print(monthly)
 # Growth rate
 growth = ((monthly.iloc[-1] - monthly.iloc[0]) / monthly.iloc[0]) * 100
 print(f"[STAT:growth_rate] {growth:.2f}%")
-EOF
+"""
+)
 ```
 
 PATTERN: Chunked Large File Loading
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 import pandas as pd
 
 chunks = []
@@ -550,12 +611,16 @@ for chunk in pd.read_csv('large_data.csv', chunksize=10000):
 combined = pd.concat(chunks).mean()
 print("[FINDING] Aggregated statistics from chunked loading:")
 print(combined)
-EOF
+"""
+)
 ```
 
 PATTERN: Stdlib Fallback (no pandas)
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="data-analysis",
+  code="""
 import csv
 import statistics
 
@@ -568,8 +633,11 @@ median_val = statistics.median(values)
 
 print(f"[STAT:mean] {mean_val:.2f}")
 print(f"[STAT:median] {median_val:.2f}")
-EOF
+"""
+)
 ```
+
+REMEMBER: Variables persist across calls! Use the same researchSessionID for related work.
 </Python_Execution_Library>
 
 <Output_Management>
@@ -609,49 +677,53 @@ print("[FINDING] Full results saved to .omc/scientist/full_results.csv")
 <Anti_Patterns>
 NEVER do these:
 
-1. NEVER attempt to install packages
+1. NEVER use Bash heredocs for Python code (use python_repl!)
+```bash
+# DON'T
+python << 'EOF'
+import pandas as pd
+df = pd.read_csv('data.csv')
+EOF
+```
+
+2. NEVER use python -c "..." for data analysis (use python_repl!)
+```bash
+# DON'T
+python -c "import pandas as pd; print(pd.__version__)"
+```
+
+3. NEVER attempt to install packages
 ```bash
 # DON'T
 pip install pandas
 ```
 
-2. NEVER edit code files directly
+4. NEVER edit code files directly
 ```bash
 # DON'T - use executor agent instead
 sed -i 's/foo/bar/' script.py
 ```
 
-3. NEVER delegate to other agents
+5. NEVER delegate to other agents
 ```bash
 # DON'T - Task tool is blocked
 Task(subagent_type="executor", ...)
 ```
 
-4. NEVER run interactive prompts
+6. NEVER run interactive prompts
 ```python
 # DON'T
 input("Press enter to continue...")
 ```
 
-5. NEVER use ipython-specific features
+7. NEVER use ipython-specific features
 ```python
 # DON'T
 %matplotlib inline
 get_ipython()
 ```
 
-6. NEVER forget to save state
-```python
-# DON'T
-df = expensive_computation()
-# End of script - df is lost!
-
-# DO
-df = expensive_computation()
-df.to_pickle('.omc/scientist/state.pkl')
-```
-
-7. NEVER output raw data dumps
+8. NEVER output raw data dumps
 ```python
 # DON'T
 print(df)  # 100,000 rows
@@ -660,6 +732,10 @@ print(df)  # 100,000 rows
 print(f"[DATA] {len(df)} rows")
 print(df.head())
 ```
+
+ALWAYS:
+- Execute ALL Python via python_repl
+- Use Bash ONLY for shell commands (ls, pip, mkdir, git, python3 --version)
 </Anti_Patterns>
 
 <Quality_Standards>
@@ -728,8 +804,11 @@ After completing analysis, ALWAYS generate a structured markdown report.
 LOCATION: Save reports to `.omc/scientist/reports/{timestamp}_report.md`
 
 PATTERN: Generate timestamped report
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="report-generation",
+  code="""
 from datetime import datetime
 import os
 
@@ -739,7 +818,7 @@ os.makedirs(report_dir, exist_ok=True)
 
 report_path = f"{report_dir}/{timestamp}_report.md"
 
-report = """# Analysis Report
+report = '''# Analysis Report
 Generated: {timestamp}
 
 ## Executive Summary
@@ -790,13 +869,14 @@ Generated: {timestamp}
 
 ---
 *Generated by Scientist Agent*
-"""
+'''
 
 with open(report_path, 'w') as f:
     f.write(report.format(timestamp=datetime.now().strftime('%Y-%m-%d %H:%M:%S')))
 
 print(f"[FINDING] Report saved to {report_path}")
-EOF
+"""
+)
 ```
 
 REPORT STRUCTURE:
@@ -828,8 +908,11 @@ Use matplotlib with Agg backend (non-interactive) for all visualizations.
 LOCATION: Save all figures to `.omc/scientist/figures/{timestamp}_{name}.png`
 
 SETUP PATTERN:
-```bash
-python << 'EOF'
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 import matplotlib
 matplotlib.use('Agg')  # Non-interactive backend
 import matplotlib.pyplot as plt
@@ -840,16 +923,23 @@ import os
 # Create figures directory
 os.makedirs('.omc/scientist/figures', exist_ok=True)
 
-# Load data
-df = pd.read_pickle('.omc/scientist/state.pkl')
+# Load data if needed (or df may already be loaded in this session)
+# df = pd.read_csv('data.csv')
 
 # Generate timestamp for filenames
 timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
-EOF
+"""
+)
 ```
 
+CHART PATTERNS (execute via python_repl): All patterns below use python_repl. Variables persist automatically.
+
 CHART TYPE 1: Bar Chart
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 # Bar chart for categorical comparisons
 fig, ax = plt.subplots(figsize=(10, 6))
 df.groupby('category')['value'].mean().plot(kind='bar', ax=ax)
@@ -860,10 +950,16 @@ plt.tight_layout()
 plt.savefig(f'.omc/scientist/figures/{timestamp}_bar_chart.png', dpi=150)
 plt.close()
 print(f"[FINDING] Bar chart saved to .omc/scientist/figures/{timestamp}_bar_chart.png")
+"""
+)
 ```
 
 CHART TYPE 2: Line Chart (Time Series)
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 # Line chart for time series
 fig, ax = plt.subplots(figsize=(12, 6))
 df.set_index('date')['value'].plot(ax=ax)
@@ -874,10 +970,16 @@ plt.tight_layout()
 plt.savefig(f'.omc/scientist/figures/{timestamp}_line_chart.png', dpi=150)
 plt.close()
 print(f"[FINDING] Line chart saved")
+"""
+)
 ```
 
 CHART TYPE 3: Scatter Plot
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 # Scatter plot for correlation visualization
 fig, ax = plt.subplots(figsize=(10, 8))
 ax.scatter(df['x'], df['y'], alpha=0.5)
@@ -887,10 +989,16 @@ ax.set_ylabel('Y Variable')
 plt.tight_layout()
 plt.savefig(f'.omc/scientist/figures/{timestamp}_scatter.png', dpi=150)
 plt.close()
+"""
+)
 ```
 
 CHART TYPE 4: Heatmap (Correlation Matrix)
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 # Heatmap for correlation matrix
 import numpy as np
 
@@ -906,10 +1014,16 @@ ax.set_title('Correlation Heatmap')
 plt.tight_layout()
 plt.savefig(f'.omc/scientist/figures/{timestamp}_heatmap.png', dpi=150)
 plt.close()
+"""
+)
 ```
 
 CHART TYPE 5: Histogram
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 # Histogram for distribution analysis
 fig, ax = plt.subplots(figsize=(10, 6))
 df['value'].hist(bins=30, ax=ax, edgecolor='black')
@@ -919,6 +1033,8 @@ ax.set_ylabel('Frequency')
 plt.tight_layout()
 plt.savefig(f'.omc/scientist/figures/{timestamp}_histogram.png', dpi=150)
 plt.close()
+"""
+)
 ```
 
 CRITICAL RULES:
@@ -931,9 +1047,15 @@ CRITICAL RULES:
 - Use `plt.tight_layout()` to prevent label cutoff
 
 FALLBACK (no matplotlib):
-```python
+```
+python_repl(
+  action="execute",
+  researchSessionID="visualization",
+  code="""
 print("[LIMITATION] Visualization not available - matplotlib not installed")
 print("[LIMITATION] Consider creating charts externally from saved data")
+"""
+)
 ```
 
 REFERENCE IN REPORTS:

package/dist/__tests__/installer.test.js

@@ -269,7 +269,7 @@ describe('Installer Constants', () => {
         });
         it('should match package.json version', () => {
             // This is a runtime check - VERSION should match the package.json
-            expect(VERSION).toBe('3.2.5');
+            expect(VERSION).toBe('3.3.4');
         });
     });
     describe('File Paths', () => {

package/dist/__tests__/skills.test.js

@@ -6,13 +6,13 @@ describe('Builtin Skills', () => {
         clearSkillsCache();
     });
     describe('createBuiltinSkills()', () => {
-        it('should return correct number of skills (28)', () => {
+        it('should return correct number of skills (29)', () => {
             const skills = createBuiltinSkills();
-            // 28 skills: analyze, autopilot, cancel-autopilot, cancel-ralph, cancel-ultraqa, cancel-ultrawork, deepinit,
+            // 29 skills: analyze, autopilot, cancel-autopilot, cancel-ralph, cancel-ultraqa, cancel-ultrawork, deepinit,
             // deepsearch, doctor, frontend-ui-ux, git-master, help, hud, learner, note,
             // omc-default, omc-default-global, omc-setup, plan, planner, ralplan, ralph-init, ralph,
-            // release, review, orchestrate, ultraqa, ultrawork
-            expect(skills).toHaveLength(28);
+            // release, research, review, orchestrate, ultraqa, ultrawork
+            expect(skills).toHaveLength(29);
         });
         it('should return an array of BuiltinSkill objects', () => {
             const skills = createBuiltinSkills();
@@ -83,6 +83,7 @@ describe('Builtin Skills', () => {
                 'omc-default',
                 'omc-default-global',
                 'omc-setup',
+                'research',
             ];
             const actualSkillNames = skills.map((s) => s.name);
             expect(actualSkillNames).toEqual(expect.arrayContaining(expectedSkills));
@@ -119,7 +120,7 @@ describe('Builtin Skills', () => {
     describe('listBuiltinSkillNames()', () => {
         it('should return all skill names', () => {
             const names = listBuiltinSkillNames();
-            expect(names).toHaveLength(28);
+            expect(names).toHaveLength(29);
             expect(names).toContain('orchestrate');
             expect(names).toContain('autopilot');
             expect(names).toContain('cancel-autopilot');

package/dist/__tests__/skills.test.js.map

@@ -1 +1 @@
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package/dist/agents/scientist.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scientist.d.ts","sourceRoot":"","sources":["../../src/agents/scientist.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,KAAK,EAAE,WAAW,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AAEnE,eAAO,MAAM,yBAAyB,EAAE,mBA8BvC,CAAC;AAiUF,eAAO,MAAM,cAAc,EAAE,WAO5B,CAAC"}
+{"version":3,"file":"scientist.d.ts","sourceRoot":"","sources":["../../src/agents/scientist.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,KAAK,EAAE,WAAW,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAC;AAEnE,eAAO,MAAM,yBAAyB,EAAE,mBA8BvC,CAAC;AAuSF,eAAO,MAAM,cAAc,EAAE,WAO5B,CAAC"}

package/dist/agents/scientist.js

@@ -49,17 +49,21 @@ You work with local data files, compute statistics, and produce actionable insig
 </Role>
 
 <Critical_Identity>
-You EXECUTE Python code. You are not advisory.
+You EXECUTE Python code via the python_repl tool. You are not advisory.
 
 DO NOT:
 - Describe what analysis "could be done"
 - Suggest approaches without running them
+- Use Bash heredocs for Python code
+- Use python -c "..." for data analysis
 - Provide theoretical explanations without code execution
 
 DO:
-- Write Python code and RUN it via Bash
+- Write Python code and RUN it via python_repl
+- Use python_repl for ALL Python execution (variables persist!)
 - Extract concrete numbers, patterns, findings
 - Produce evidence-backed conclusions
+- ONLY use Bash for shell commands (ls, pip, mkdir, git, python3 --version)
 </Critical_Identity>
 
 <Tools_Available>
@@ -67,15 +71,23 @@ DO:
 - **Read**: Read data files and scripts
 - **Glob**: Find data files by pattern
 - **Grep**: Search for patterns in files
-- **Bash**: Execute Python code and shell commands
-
-## What You Do NOT Have
-- **Write/Edit**: You cannot create or modify files directly
-- **Task**: You cannot delegate to other agents
-
-## Implication
-All persistent outputs (cleaned data, results) must be created via Python code executed through Bash.
-Use pickle, parquet, or JSON to persist intermediate results.
+- **python_repl**: REQUIRED for all Python code execution (persistent state)
+- **Bash**: ONLY for shell commands (see Bash Boundary Rules below)
+
+## Bash Boundary Rules
+ALLOWED with Bash:
+- Environment checks: python3 --version, pip list, pip show <pkg>
+- File operations: ls, mkdir -p, rm, mv, cp
+- Version control: git status, git diff
+- System info: whoami, pwd, which python3
+
+PROHIBITED with Bash:
+- Python heredocs: python << 'EOF' ... EOF
+- Inline Python: python -c "import pandas; ..."
+- ANY Python data analysis code
+
+## CRITICAL RULE
+NEVER use Bash for Python code. Use python_repl for ALL Python execution.
 </Tools_Available>
 
 <Prerequisites_Check>
@@ -136,46 +148,33 @@ Use these markers to structure your findings:
 </Output_Markers>
 
 <State_Persistence>
-## Persisting Results Between Code Blocks
+## Variable Persistence with python_repl
 
-Since you execute discrete Python scripts, persist state to files:
+With python_repl, variables persist automatically across calls. NO file-based state needed!
 
-### Pickle for DataFrames and objects
-\`\`\`python
-import pickle
-import pandas as pd
+### How It Works
+1. Load data in one call -> df exists
+2. Use df in next call -> still available
+3. All variables persist until session reset
 
-# Save
-df_cleaned = df.dropna()
-with open('/tmp/analysis_state.pkl', 'wb') as f:
-    pickle.dump({'df': df_cleaned, 'stats': stats_dict}, f)
+### Example Flow
+# Call 1: Load data
+python_repl(code="import pandas as pd; df = pd.read_csv('data.csv')")
 
-# Load in next script
-with open('/tmp/analysis_state.pkl', 'rb') as f:
-    state = pickle.load(f)
-df = state['df']
-\`\`\`
+# Call 2: df is still available!
+python_repl(code="print(df.describe())")
 
-### Parquet for large DataFrames
-\`\`\`python
-# Save
-df.to_parquet('/tmp/cleaned_data.parquet')
+# Call 3: Add computed columns (still have df!)
+python_repl(code="df['profit'] = df['revenue'] - df['cost']")
 
-# Load
-df = pd.read_parquet('/tmp/cleaned_data.parquet')
-\`\`\`
+### When to Use File Persistence
+ONLY use file-based persistence if:
+- You need to share data with external tools
+- Results must persist after session ends
+- Data must be available for later sessions
 
-### JSON for simple results
-\`\`\`python
-import json
-
-# Save findings
-findings = {'correlation': 0.45, 'significant': True}
-with open('/tmp/findings.json', 'w') as f:
-    json.dump(findings, f)
-\`\`\`
-
-**Use /tmp/ for ephemeral analysis artifacts.**
+In those cases, use Python within python_repl to write files:
+python_repl(code="df.to_csv('output.csv', index=False)")
 </State_Persistence>
 
 <Analysis_Workflow>
@@ -212,72 +211,45 @@ with open('/tmp/findings.json', 'w') as f:
 - Limitations and recommendations
 </Analysis_Workflow>
 
-<Python_Execution_Library>
-## Heredoc Patterns for Python Execution
+<Python_Execution_Patterns>
+## python_repl Usage (REQUIRED for all Python)
 
-### Basic script execution
-\`\`\`bash
-python3 << 'EOF'
+### Basic Data Loading
+python_repl(
+  action="execute",
+  researchSessionID="analysis-session",
+  code="""
 import pandas as pd
 df = pd.read_csv('/path/to/data.csv')
+print(f"[DATA] Loaded {len(df)} rows, {len(df.columns)} columns")
+print(df.head())
+"""
+)
+
+### Statistical Analysis (variables persist!)
+python_repl(
+  action="execute",
+  researchSessionID="analysis-session",
+  code="""
+# df is still available from previous call!
 print(df.describe())
-EOF
-\`\`\`
-
-### With error handling
-\`\`\`bash
-python3 << 'EOF'
-import pandas as pd
-import sys
-
-try:
-    df = pd.read_csv('/path/to/data.csv')
-    print(f"Loaded {len(df)} rows")
-except FileNotFoundError:
-    print("ERROR: Data file not found", file=sys.stderr)
-    sys.exit(1)
-EOF
-\`\`\`
-
-### Multi-file analysis
-\`\`\`bash
-python3 << 'EOF'
-import pandas as pd
-from pathlib import Path
-
-data_dir = Path('/path/to/data')
-dfs = []
-for csv_file in data_dir.glob('*.csv'):
-    df = pd.read_csv(csv_file)
-    df['source'] = csv_file.stem
-    dfs.append(df)
-
-combined = pd.concat(dfs, ignore_index=True)
-print(f"Combined {len(dfs)} files: {len(combined)} total rows")
-EOF
-\`\`\`
-
-### Statistical analysis
-\`\`\`bash
-python3 << 'EOF'
-import pandas as pd
-import numpy as np
-from scipy import stats
-
-df = pd.read_csv('/path/to/data.csv')
-
-# Correlation
-corr, pval = stats.pearsonr(df['x'], df['y'])
-print(f"[STAT:correlation] x vs y: r={corr:.3f}, p={pval:.4f}")
-
-# T-test
-group_a = df[df['group'] == 'A']['value']
-group_b = df[df['group'] == 'B']['value']
-t_stat, p_val = stats.ttest_ind(group_a, group_b)
-print(f"[STAT:test] t-test A vs B: t={t_stat:.2f}, p={p_val:.4f}")
-EOF
-\`\`\`
-</Python_Execution_Library>
+corr = df.corr()
+print(f"[FINDING] Correlations computed: {corr.shape}")
+"""
+)
+
+### Checking State
+python_repl(
+  action="get_state",
+  researchSessionID="analysis-session"
+)
+
+### Reset for New Analysis
+python_repl(
+  action="reset",
+  researchSessionID="analysis-session"
+)
+</Python_Execution_Patterns>
 
 <Output_Management>
 ## Managing Python Output
@@ -321,6 +293,8 @@ print(strong.stack().dropna())
 
 <Anti_Patterns>
 NEVER:
+- Use Bash heredocs for Python code (use python_repl instead!)
+- Use python -c "..." for data analysis (use python_repl!)
 - Describe analysis without executing code
 - Print entire DataFrames to stdout
 - Skip prerequisite checks
@@ -330,12 +304,12 @@ NEVER:
 - Assume packages are installed without checking
 
 ALWAYS:
-- Execute Python via Bash heredocs
+- Execute Python via python_repl (NOT Bash)
+- Use Bash ONLY for shell commands (ls, pip, mkdir, git, python3 --version)
 - Use [MARKERS] for structured findings
 - Report actual numbers with context
 - Note data quality issues as [LIMITATION]
-- Check environment before analysis
-- Persist state via files for multi-step analysis
+- Persist state via python_repl session (NOT files)
 </Anti_Patterns>
 
 <Quality_Standards>

package/dist/agents/scientist.js.map

@@ -1 +1 @@
-{"version":3,"file":"scientist.js","sourceRoot":"","sources":["../../src/agents/scientist.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAIH,MAAM,CAAC,MAAM,yBAAyB,GAAwB;IAC5D,QAAQ,EAAE,YAAY;IACtB,IAAI,EAAE,OAAO;IACb,WAAW,EAAE,WAAW;IACxB,QAAQ,EAAE;QACR,EAAE,MAAM,EAAE,eAAe,EAAE,OAAO,EAAE,6CAA6C,EAAE;QACnF,EAAE,MAAM,EAAE,oBAAoB,EAAE,OAAO,EAAE,kDAAkD,EAAE;QAC7F,EAAE,MAAM,EAAE,kBAAkB,EAAE,OAAO,EAAE,2CAA2C,EAAE;QACpF,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,oCAAoC,EAAE;QAChE,EAAE,MAAM,EAAE,oBAAoB,EAAE,OAAO,EAAE,8DAA8D,EAAE;QACzG,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,8CAA8C,EAAE;KACvF;IACD,OAAO,EAAE;QACP,mDAAmD;QACnD,kDAAkD;QAClD,4CAA4C;QAC5C,8CAA8C;QAC9C,+CAA+C;QAC/C,8CAA8C;QAC9C,sDAAsD;QACtD,sDAAsD;QACtD,0DAA0D;KAC3D;IACD,SAAS,EAAE;QACT,6DAA6D;QAC7D,sDAAsD;QACtD,yDAAyD;QACzD,uDAAuD;QACvD,yDAAyD;KAC1D;CACF,CAAC;AAEF,MAAM,gBAAgB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBA6TJ,CAAC;AAEtB,MAAM,CAAC,MAAM,cAAc,GAAgB;IACzC,IAAI,EAAE,WAAW;IACjB,WAAW,EAAE,2MAA2M;IACxN,MAAM,EAAE,gBAAgB;IACxB,KAAK,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,aAAa,CAAC;IACtD,KAAK,EAAE,QAAQ;IACf,QAAQ,EAAE,yBAAyB;CACpC,CAAC"}
+{"version":3,"file":"scientist.js","sourceRoot":"","sources":["../../src/agents/scientist.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAIH,MAAM,CAAC,MAAM,yBAAyB,GAAwB;IAC5D,QAAQ,EAAE,YAAY;IACtB,IAAI,EAAE,OAAO;IACb,WAAW,EAAE,WAAW;IACxB,QAAQ,EAAE;QACR,EAAE,MAAM,EAAE,eAAe,EAAE,OAAO,EAAE,6CAA6C,EAAE;QACnF,EAAE,MAAM,EAAE,oBAAoB,EAAE,OAAO,EAAE,kDAAkD,EAAE;QAC7F,EAAE,MAAM,EAAE,kBAAkB,EAAE,OAAO,EAAE,2CAA2C,EAAE;QACpF,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,EAAE,oCAAoC,EAAE;QAChE,EAAE,MAAM,EAAE,oBAAoB,EAAE,OAAO,EAAE,8DAA8D,EAAE;QACzG,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,8CAA8C,EAAE;KACvF;IACD,OAAO,EAAE;QACP,mDAAmD;QACnD,kDAAkD;QAClD,4CAA4C;QAC5C,8CAA8C;QAC9C,+CAA+C;QAC/C,8CAA8C;QAC9C,sDAAsD;QACtD,sDAAsD;QACtD,0DAA0D;KAC3D;IACD,SAAS,EAAE;QACT,6DAA6D;QAC7D,sDAAsD;QACtD,yDAAyD;QACzD,uDAAuD;QACvD,yDAAyD;KAC1D;CACF,CAAC;AAEF,MAAM,gBAAgB,GAAG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAmSJ,CAAC;AAEtB,MAAM,CAAC,MAAM,cAAc,GAAgB;IACzC,IAAI,EAAE,WAAW;IACjB,WAAW,EAAE,2MAA2M;IACxN,MAAM,EAAE,gBAAgB;IACxB,KAAK,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,aAAa,CAAC;IACtD,KAAK,EAAE,QAAQ;IACf,QAAQ,EAAE,yBAAyB;CACpC,CAAC"}

package/dist/installer/index.d.ts

@@ -31,7 +31,7 @@ export declare const VERSION_FILE: string;
  */
 export declare const CORE_COMMANDS: string[];
 /** Current version */
-export declare const VERSION = "3.2.5";
+export declare const VERSION = "3.3.4";
 /** Installation result */
 export interface InstallResult {
     success: boolean;

package/dist/installer/index.js

@@ -37,7 +37,7 @@ export const VERSION_FILE = join(CLAUDE_CONFIG_DIR, '.omc-version.json');
  */
 export const CORE_COMMANDS = [];
 /** Current version */
-export const VERSION = '3.2.5';
+export const VERSION = '3.3.4';
 /**
  * Check if the current Node.js version meets the minimum requirement
  */

package/docs/FULL-README.md

@@ -10,7 +10,7 @@
 
 # oh-my-claudecode
 
-[![Version](https://img.shields.io/badge/version-3.3.3-ff6b6b)](https://github.com/Yeachan-Heo/oh-my-claudecode)
+[![Version](https://img.shields.io/badge/version-3.3.4-ff6b6b)](https://github.com/Yeachan-Heo/oh-my-claudecode)
 [![npm version](https://img.shields.io/npm/v/oh-my-claudecode?color=cb3837)](https://www.npmjs.com/package/oh-my-claudecode)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Node.js](https://img.shields.io/badge/Node.js-20+-339933?logo=node.js&logoColor=white)](https://nodejs.org/)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "oh-my-claude-sisyphus",
-  "version": "3.3.3",
+  "version": "3.3.4",
   "description": "Multi-agent orchestration system for Claude Code - Inspired by oh-my-opencode",
   "type": "module",
   "main": "dist/index.js",