claude-turing 4.8.0 → 4.8.1

package/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "turing",
-  "version": "4.8.0",
+  "version": "4.8.1",
   "description": "Autonomous ML research harness — the autoresearch loop as a formal protocol. 74 commands, 2 specialized agents, skills/turing source layout, operational intelligence (postmortem + doctor + plan), model lifecycle (update + registry), what-if analysis (whatif + counterfactual + simulate), collaboration (onboard + share + review), research communication (cite + present + changelog), experiment archaeology (trend + flashback + archive + annotate + search + template + replay), model surgery (prune + quantize + merge + surgery), feature & training intelligence, model debugging, pre-training intelligence, meta-intelligence, scaling & efficiency, model composition, deep analysis, experiment orchestration, literature + paper, model export, profiling, checkpoints, experiment intelligence, statistical rigor, tree-search, cost-performance, model cards, hypothesis database, novelty guard, anti-cheating, taste-leverage loop. Inspired by Karpathy's autoresearch and the scientific method itself.",
   "author": {
     "name": "Prannaya Gupta"

package/README.md

@@ -3,7 +3,7 @@
 *The research assistant that can't fool itself.*
 
 <p align="center">
-  <img src="https://img.shields.io/badge/version-4.8.0-ffb74d?style=flat-square&labelColor=1a1a2e" alt="Version" />
+  <img src="https://img.shields.io/badge/version-4.8.1-ffb74d?style=flat-square&labelColor=1a1a2e" alt="Version" />
   <img src="https://img.shields.io/badge/license-MIT-ff4d4d?style=flat-square&labelColor=1a1a2e" alt="License" /> 
   <img src="https://img.shields.io/badge/Claude_Code-plugin-ff4d4d?style=flat-square&labelColor=1a1a2e" alt="Claude Code" /> 
   <img src="https://img.shields.io/badge/Node.js-20%2B-ff4d4d?style=flat-square&labelColor=1a1a2e" alt="Node.js" />

package/agents/ml-evaluator.md

@@ -22,13 +22,13 @@ In quantum mechanics, observation changes the system. In ML experimentation, the
 
 ## Useful Commands
 
-Always activate the venv first: `source .venv/bin/activate`
+Always run Python through uv from the ML directory.
 
 | Command | Purpose |
 |---------|---------|
-| `python scripts/show_metrics.py --last 10` | Recent experiment summary |
-| `python scripts/compare_runs.py <a> <b>` | Side-by-side comparison |
-| `python evaluate.py` | Run evaluation on current model |
+| `uv run python scripts/show_metrics.py --last 10` | Recent experiment summary |
+| `uv run python scripts/compare_runs.py <a> <b>` | Side-by-side comparison |
+| `uv run python evaluate.py` | Run evaluation on current model |
 | `cat experiments/results.tsv` | Quick-reference TSV |
 
 ## Analysis Framework

package/agents/ml-researcher.md

@@ -27,8 +27,8 @@ Read `program.md` in the ML directory for the complete experiment loop protocol.
 ## Constraints
 
 - **Only modify `train.py` and `config.yaml`.** `evaluate.py` is HIDDEN (do not read or reference). Other pipeline files are READ-ONLY.
-- **Always work in the venv:** `source .venv/bin/activate`
-- **Redirect training output:** `python train.py > run.log 2>&1`
+- **Always run Python through uv:** `uv run python ...`
+- **Redirect training output:** `uv run python train.py > run.log 2>&1`
 - **Parse metrics with grep:** `grep -A 10 "^---" run.log | head -10`
 - **Use @ml-evaluator** for analysis tasks — it has no Write/Edit tools and cannot accidentally break the pipeline.
 

package/bin/turing-init.sh

@@ -33,8 +33,8 @@ echo ""
 if [[ $# -eq 0 ]] || [[ "${1:-}" == "--interactive" ]]; then
     python3 "$SCAFFOLD_SCRIPT" --interactive --templates-dir "$TEMPLATES_DIR" --no-venv
     echo ""
-    echo "  To set up the virtual environment:"
-    echo "    cd <ml_dir> && python3 -m venv .venv && source .venv/bin/activate && pip install -r requirements.txt"
+    echo "  To set up the uv environment:"
+    echo "    cd <ml_dir> && uv sync"
     exit 0
 fi
 

package/commands/ablate.md

@@ -9,9 +9,9 @@ Run a systematic ablation study to measure the contribution of each model compon
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Run a systematic ablation study to measure the contribution of each model compon
 
 3. **Run ablation study:**
    ```bash
-   python scripts/ablation_study.py $ARGUMENTS
+   uv run python scripts/ablation_study.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/annotate.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Add context that experiment logs can't capture. "This only worked because the data was pre-sorted."
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_annotations.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_annotations.py $ARGUMENTS`
 3. **Operations:** add (text + tags), list (per-experiment or all), search (keyword or tag)
 4. **Stored in:** `experiments/annotations.yaml`
 

package/commands/archive.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Keep your project directory manageable after 200+ experiments.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_archive.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_archive.py $ARGUMENTS`
 3. **Protected experiments:** Pareto-optimal, current best, recent, top-N by metric
 4. **Report:** archived count, preserved count, space reclaimed
 5. **Saved output:** `experiments/archive/index.yaml`

package/commands/audit.md

@@ -9,9 +9,9 @@ A reviewer checklist you run before submitting. Catches methodology mistakes tha
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ A reviewer checklist you run before submitting. Catches methodology mistakes tha
 
 3. **Run methodology audit:**
    ```bash
-   python scripts/methodology_audit.py $ARGUMENTS
+   uv run python scripts/methodology_audit.py $ARGUMENTS
    ```
 
 4. **Checks performed:**

package/commands/baseline.md

@@ -9,9 +9,9 @@ Generate trivial baselines so you always know if your model is meaningfully bett
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Generate trivial baselines so you always know if your model is meaningfully bett
 
 3. **Run baseline generation:**
    ```bash
-   python scripts/generate_baselines.py $ARGUMENTS
+   uv run python scripts/generate_baselines.py $ARGUMENTS
    ```
 
 4. **Baselines generated:**

package/commands/brief.md

@@ -2,7 +2,7 @@
 name: brief
 description: Generate a structured research intelligence report from experiment history — what's been learned, what's promising, what's exhausted, and what the human should consider next. Use --deep for literature-grounded suggestions.
 argument-hint: "[ml/project] [--deep]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob, WebSearch, WebFetch
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob, WebSearch, WebFetch
 ---
 
 Generate a research briefing that a human can read in 2 minutes and immediately decide what to inject next.
@@ -23,14 +23,14 @@ Before generating the briefing, detect which project to report on:
 
 1. **Generate the briefing:**
    ```bash
-   source .venv/bin/activate && python scripts/generate_brief.py
+   uv run python scripts/generate_brief.py
    ```
 
 2. **Self-critique the briefing** before presenting. Review the generated output and check:
    - **Recommendations specificity:** Are they concrete enough to act on? "Try a different model" is bad. "Try LightGBM with leaf-wise growth because exp-004 showed depth sensitivity" is good. If vague, rewrite them with specific model/hyperparameter suggestions grounded in the experiment data.
    - **Exhausted directions coverage:** Cross-reference the "Model Types Explored" section against `experiments/log.jsonl`. Are there discarded experiments missing from the summary? If so, add them.
    - **Convergence estimate grounding:** If the briefing says "close to convergence" or "further improvement possible", verify against the actual metric trajectory. Is the claim supported by the numbers?
-   - **Metric accuracy:** Spot-check that the "Current Best" metrics match the actual log. Run `python scripts/show_metrics.py --last 1` if uncertain.
+   - **Metric accuracy:** Spot-check that the "Current Best" metrics match the actual log. Run `uv run python scripts/show_metrics.py --last 1` if uncertain.
 
    If any section fails the check, regenerate just that section. Max 1 revision round — don't over-polish.
 
@@ -75,7 +75,7 @@ When `--deep` is requested, add a 7th section: **Literature-Grounded Suggestions
 
 4. **Queue suggestions** as hypotheses:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add "<technique>: <rationale> (source: <citation>)" --priority medium --source literature
+   uv run python scripts/manage_hypotheses.py add "<technique>: <rationale> (source: <citation>)" --priority medium --source literature
    ```
 
 5. **Format as a section** appended to the briefing.
@@ -83,7 +83,7 @@ When `--deep` is requested, add a 7th section: **Literature-Grounded Suggestions
 ## Saving Briefs
 
 ```bash
-mkdir -p briefs && python scripts/generate_brief.py > briefs/brief-$(date +%Y-%m-%d).md
+mkdir -p briefs && uv run python scripts/generate_brief.py > briefs/brief-$(date +%Y-%m-%d).md
 ```
 
 ## When to Use

package/commands/budget.md

@@ -9,9 +9,9 @@ Set a compute ceiling and let the system optimize within it. Prevents runaway ex
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Set a compute ceiling and let the system optimize within it. Prevents runaway ex
 
 3. **Run budget manager:**
    ```bash
-   python scripts/budget_manager.py $ARGUMENTS
+   uv run python scripts/budget_manager.py $ARGUMENTS
    ```
 
 4. **Actions:**

package/commands/calibrate.md

@@ -9,9 +9,9 @@ Make model probabilities trustworthy. Does 80% confidence actually mean 80% corr
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Make model probabilities trustworthy. Does 80% confidence actually mean 80% corr
 
 3. **Run calibration:**
    ```bash
-   python scripts/calibration.py $ARGUMENTS
+   uv run python scripts/calibration.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/card.md

@@ -1,7 +1,7 @@
 ---
 name: card
 description: Generate a standardized model card documenting the trained model — type, performance, training data, limitations, intended use, and artifact contract.
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob
 ---
 
 You generate a standardized model card from the experiment log, model contract, and config.
@@ -10,12 +10,12 @@ You generate a standardized model card from the experiment log, model contract,
 
 1. **Activate the virtual environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Run the model card generator:**
    ```bash
-   python scripts/generate_model_card.py --config config.yaml --log experiments/log.jsonl --contract model_contract.md --output MODEL_CARD.md
+   uv run python scripts/generate_model_card.py --config config.yaml --log experiments/log.jsonl --contract model_contract.md --output MODEL_CARD.md
    ```
 
 3. **Read and present the generated card:**

package/commands/changelog.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Translate experiment logs into a narrative that PMs and stakeholders can read in 2 minutes.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/generate_changelog.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/generate_changelog.py $ARGUMENTS`
 3. **Audience:** technical (experiment IDs, configs), stakeholder (plain English, percentages)
 4. **Saved output:** `paper/CHANGELOG.md`
 

package/commands/checkpoint.md

@@ -9,9 +9,9 @@ Manage model checkpoints intelligently using Pareto dominance.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Manage model checkpoints intelligently using Pareto dominance.
 
 3. **Run checkpoint manager:**
    ```bash
-   python scripts/checkpoint_manager.py $ARGUMENTS
+   uv run python scripts/checkpoint_manager.py $ARGUMENTS
    ```
 
 4. **Report results by action:**

package/commands/cite.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Track which papers and methods influenced each experiment. Catch missing citations before submission.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/citation_manager.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/citation_manager.py $ARGUMENTS`
 3. **Operations:** add (associate citation with experiment), list (group by type), check (audit missing), bib (BibTeX)
 4. **Stored in:** `experiments/citations.yaml`
 

package/commands/compare.md

@@ -11,7 +11,7 @@ Compare two ML experiment runs side-by-side to understand what changed and why o
 
 1. **Run comparison:**
    ```bash
-   source .venv/bin/activate && python scripts/compare_runs.py $0 $1
+   uv run python scripts/compare_runs.py $0 $1
    ```
 
 2. **Analyze the delta:**

package/commands/counterfactual.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 What would need to change to flip this prediction? Minimum-change counterfactual for individual predictions.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/counterfactual_explanation.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/counterfactual_explanation.py $ARGUMENTS`
 3. **Saved:** `experiments/counterfactuals/`
 
 ## Methods

package/commands/curriculum.md

@@ -9,9 +9,9 @@ Does the order your model sees data matter? Find out systematically.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Does the order your model sees data matter? Find out systematically.
 
 3. **Run curriculum analysis:**
    ```bash
-   python scripts/curriculum_optimizer.py $ARGUMENTS
+   uv run python scripts/curriculum_optimizer.py $ARGUMENTS
    ```
 
 4. **Strategies tested:**

package/commands/design.md

@@ -2,7 +2,7 @@
 name: design
 description: Generate a structured experiment design for a hypothesis. Reads experiment history, searches literature for methodology, produces a scored design document at experiments/designs/.
 argument-hint: "<hypothesis-id or description>"
-allowed-tools: Read, Write, Bash(python scripts/*:*, source .venv/bin/activate:*, mkdir:*), Grep, Glob, WebSearch, WebFetch
+allowed-tools: Read, Write, Bash(uv run python scripts/*:*, uv sync:*, mkdir:*), Grep, Glob, WebSearch, WebFetch
 ---
 
 Front-load the thinking before the coding. Given a hypothesis, produce a structured experiment design grounded in methodology from the literature.
@@ -13,7 +13,7 @@ Front-load the thinking before the coding. Given a hypothesis, produce a structu
 
 If `$ARGUMENTS` matches `hyp-NNN`, load the hypothesis:
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py show $ARGUMENTS
+uv run python scripts/manage_hypotheses.py show $ARGUMENTS
 ```
 
 If freeform text, use it directly as the hypothesis description.
@@ -23,7 +23,7 @@ Read the current config and experiment state:
 cat config.yaml
 ```
 ```bash
-source .venv/bin/activate && python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
+uv run python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
 ```
 ```bash
 cat experiment_state.yaml 2>/dev/null || echo "No experiment state yet"

package/commands/diagnose.md

@@ -9,15 +9,15 @@ Analyze where and why the model fails, beyond aggregate metrics.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Generate predictions if needed:**
    Check if `experiments/predictions/exp-NNN-preds.yaml` exists. If not, run:
    ```bash
-   python train.py --predict-only --output experiments/predictions/
+   uv run python train.py --predict-only --output experiments/predictions/
    ```
    The predictions file must contain `y_true`, `y_pred`, `task_type`, and optionally `features`.
 
@@ -28,7 +28,7 @@ Analyze where and why the model fails, beyond aggregate metrics.
 
 4. **Run error analysis:**
    ```bash
-   python scripts/diagnose_errors.py $ARGUMENTS
+   uv run python scripts/diagnose_errors.py $ARGUMENTS
    ```
 
 5. **Report results:**

package/commands/diff.md

@@ -9,9 +9,9 @@ Deep diagnostic comparison of two experiments. Goes beyond "which metric is high
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Deep diagnostic comparison of two experiments. Goes beyond "which metric is high
 
 3. **Run deep comparison:**
    ```bash
-   python scripts/experiment_diff.py $ARGUMENTS
+   uv run python scripts/experiment_diff.py $ARGUMENTS
    ```
 
 4. **Report results — the diff includes:**

package/commands/distill.md

@@ -9,9 +9,9 @@ Compress a large model into a smaller, faster one for production. Measures the a
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Compress a large model into a smaller, faster one for production. Measures the a
 
 3. **Run distillation planner:**
    ```bash
-   python scripts/model_distiller.py $ARGUMENTS
+   uv run python scripts/model_distiller.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/doctor.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Is Turing healthy? Check everything and get a score.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/harness_doctor.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/harness_doctor.py $ARGUMENTS`
 3. **Saved:** `experiments/doctor/`
 
 ## Checks

package/commands/ensemble.md

@@ -9,9 +9,9 @@ Build ensembles from your best experiments automatically. Often yields 1-3% impr
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Build ensembles from your best experiments automatically. Often yields 1-3% impr
 
 3. **Run ensemble construction:**
    ```bash
-   python scripts/build_ensemble.py $ARGUMENTS
+   uv run python scripts/build_ensemble.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/explore.md

@@ -2,7 +2,7 @@
 name: explore
 description: Tree-search-guided hypothesis exploration using AB-MCTS. Explores the space of experiment ideas as a search tree, scored by the critique engine. Discovers non-obvious refinement chains that linear suggestion cannot find.
 argument-hint: "[ml/project] [--iterations N] [--top N] [--strategy abmcts-a|abmcts-m|greedy]"
-allowed-tools: Read, Write, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob
+allowed-tools: Read, Write, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob
 ---
 
 Explore the hypothesis space using tree search. Instead of suggesting independent ideas, this builds and searches a tree of refinement chains — each node is a hypothesis scored by novelty, feasibility, and expected impact.
@@ -31,7 +31,7 @@ Extract from `$ARGUMENTS`:
 ### 1. Assess Current State
 
 ```bash
-source .venv/bin/activate && python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
+uv run python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
 ```
 
 Read `config.yaml` to understand the current model and metric.
@@ -39,7 +39,7 @@ Read `config.yaml` to understand the current model and metric.
 ### 2. Run Tree Search
 
 ```bash
-source .venv/bin/activate && python scripts/treequest_suggest.py \
+uv run python scripts/treequest_suggest.py \
     --log experiments/log.jsonl \
     --config config.yaml \
     --top <N> \
@@ -58,7 +58,7 @@ The script will:
 For each result, add to the hypothesis queue:
 
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py add "<description>" \
+uv run python scripts/manage_hypotheses.py add "<description>" \
     --priority medium --source treequest
 ```
 

package/commands/export.md

@@ -9,9 +9,9 @@ Export a trained model to a production-ready format.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Export a trained model to a production-ready format.
 
 3. **Run export pipeline:**
    ```bash
-   python scripts/export_model.py $ARGUMENTS
+   uv run python scripts/export_model.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/feature.md

@@ -9,9 +9,9 @@ Systematically evaluate which features matter and which are noise.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Systematically evaluate which features matter and which are noise.
 
 3. **Run feature analysis:**
    ```bash
-   python scripts/feature_intelligence.py $ARGUMENTS
+   uv run python scripts/feature_intelligence.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/flashback.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Come back to a project after a week and start working in 10 seconds instead of 30 minutes.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/session_flashback.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/session_flashback.py $ARGUMENTS`
 3. **Report:** current best, last session experiments, pending hypotheses, annotations, budget, suggested next action
 4. **Saved output:** `experiments/flashbacks/flashback-*.yaml`
 

package/commands/fork.md

@@ -9,9 +9,9 @@ Fork an experiment into parallel branches and compare results.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Fork an experiment into parallel branches and compare results.
 
 3. **Run fork:**
    ```bash
-   python scripts/fork_experiment.py $ARGUMENTS
+   uv run python scripts/fork_experiment.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/frontier.md

@@ -9,9 +9,9 @@ Visualize the Pareto frontier across multiple objectives from experiment history
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Visualize the Pareto frontier across multiple objectives from experiment history
 
 3. **Run Pareto analysis:**
    ```bash
-   python scripts/pareto_frontier.py $ARGUMENTS
+   uv run python scripts/pareto_frontier.py $ARGUMENTS
    ```
 
 4. **Report results:**