claude-turing 4.7.0 → 4.8.1

package/commands/replay.md

@@ -1,7 +1,6 @@
 ---
 name: replay
 description: Experiment replay — re-run a historical experiment with current infrastructure to test if old approaches do better now.
-disable-model-invocation: true
 argument-hint: "<exp-id> [--with-current-data] [--with-current-preprocessing]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Should you revisit old ideas? Infrastructure changes may make failed approaches work now.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_replay.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_replay.py $ARGUMENTS`
 3. **Modes:** default (current code+data), --with-current-data, --with-current-preprocessing
 4. **Report:** original vs replayed metrics, delta, verdict
 5. **Saved output:** `experiments/replays/`

package/commands/report.md

@@ -1,9 +1,8 @@
 ---
 name: report
 description: Generate a markdown research report from experiment history — structured for sharing, archiving, or including in documentation. More detailed than a brief, less visual than a poster.
-disable-model-invocation: true
 argument-hint: "[--since YYYY-MM-DD] [--output path]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*, mkdir:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*, mkdir:*), Grep, Glob
 ---
 
 Generate a structured markdown research report summarizing the experiment campaign.
@@ -15,12 +14,12 @@ Generate a structured markdown research report summarizing the experiment campai
 Use the logbook generator in markdown mode as the data backbone:
 
 ```bash
-source .venv/bin/activate && python scripts/generate_logbook.py --format markdown
+uv run python scripts/generate_logbook.py --format markdown
 ```
 
 Also gather supplementary data:
 ```bash
-source .venv/bin/activate && python scripts/generate_brief.py
+uv run python scripts/generate_brief.py
 cat experiment_state.yaml 2>/dev/null || true
 cat RESEARCH_PLAN.md 2>/dev/null || true
 ```

package/commands/reproduce.md

@@ -1,7 +1,6 @@
 ---
 name: reproduce
 description: Verify reproducibility of a specific experiment by re-running from logged config and checking metrics fall within tolerance.
-disable-model-invocation: true
 argument-hint: "<exp-id> [--tolerance 0.02] [--strict] [--runs 3]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Verify that a logged experiment can be reproduced with consistent results.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +22,7 @@ Verify that a logged experiment can be reproduced with consistent results.
 
 3. **Run reproducibility verification:**
    ```bash
-   python scripts/reproduce_experiment.py $ARGUMENTS
+   uv run python scripts/reproduce_experiment.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/retry.md

@@ -1,7 +1,6 @@
 ---
 name: retry
 description: Smart failure recovery — auto-diagnose crash type and retry with targeted fix. OOM → halve batch. NaN → add clipping.
-disable-model-invocation: true
 argument-hint: "<exp-id> [--max-attempts 3]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Auto-diagnose and recover from experiment failures.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +21,7 @@ Auto-diagnose and recover from experiment failures.
 
 3. **Run smart retry:**
    ```bash
-   python scripts/smart_retry.py $ARGUMENTS
+   uv run python scripts/smart_retry.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/review.md

@@ -1,7 +1,6 @@
 ---
 name: review
 description: Peer review simulation — generate likely reviewer objections with severity ratings and fix commands.
-disable-model-invocation: true
 argument-hint: "[--venue neurips|icml|general] [--harsh]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Simulate a conference reviewer before you submit. Each weakness links to the command that fixes it.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/simulate_review.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/simulate_review.py $ARGUMENTS`
 3. **Saved:** `experiments/reviews/`
 
 ## Examples

package/commands/rules/loop-protocol.md

@@ -16,9 +16,9 @@ The autoresearch harness enforces a strict separation between the **hypothesis s
 
 ## Execution Rules
 
-- **ALWAYS redirect training output:** `python train.py > run.log 2>&1`
+- **ALWAYS redirect training output:** `uv run python train.py > run.log 2>&1`
 - **ALWAYS parse metrics with grep** between `---` delimiters: `grep -A 10 "^---" run.log | head -10`
-- **ALWAYS activate the venv first:** `source .venv/bin/activate`
+- **ALWAYS run Python through uv:** `uv run python ...`
 - **NEVER install new packages** without human approval
 
 ## Git Discipline
@@ -40,16 +40,16 @@ The autoresearch harness enforces a strict separation between the **hypothesis s
 
 ## Sweep Workflow
 
-1. Generate queue: `python scripts/sweep.py`
-2. Check status: `python scripts/sweep.py --status`
-3. Get next: `python scripts/sweep.py --next`
+1. Generate queue: `uv run python scripts/sweep.py`
+2. Check status: `uv run python scripts/sweep.py --status`
+3. Get next: `uv run python scripts/sweep.py --next`
 4. Apply overrides, create branch, run training
-5. Mark: `python scripts/sweep.py --mark <name> complete|failed`
+5. Mark: `uv run python scripts/sweep.py --mark <name> complete|failed`
 6. Repeat until queue is empty
 
 ## Logging Rules
 
-- **Log every experiment** to `experiments/log.jsonl` via `python scripts/log_experiment.py` — kept and discarded alike.
+- **Log every experiment** to `experiments/log.jsonl` via `uv run python scripts/log_experiment.py` — kept and discarded alike.
 - **Include all metrics, config, and description** of the hypothesis and its outcome.
 
 ## Convergence Rules
@@ -64,11 +64,11 @@ The researcher agent's Bash access is restricted to a whitelist of necessary com
 
 | Allowed Pattern | Purpose |
 |-----------------|---------|
-| `python train.py:*` | Execute training |
-| `python scripts/*:*` | Run utility scripts (logging, metrics, sweep) |
+| `uv run python train.py:*` | Execute training |
+| `uv run python scripts/*:*` | Run utility scripts (logging, metrics, sweep) |
 | `git:*` | Branch, commit, merge, reset operations |
-| `source .venv/bin/activate:*` | Virtual environment activation |
-| `pip:*` | Package installation (requires human approval) |
+| `uv sync:*` | Virtual environment activation |
+| `uv add:*` | Package installation (requires human approval) |
 
 **Blocked by omission:** `cat`, `head`, `tail`, `less` (prevents reading hidden files via shell), `curl`, `wget` (prevents data exfiltration), arbitrary command execution.
 

package/commands/sanity.md

@@ -1,7 +1,6 @@
 ---
 name: sanity
 description: Pre-training sanity checks — catch broken data loaders, misconfigured losses, and dead gradients in 30 seconds before wasting hours.
-disable-model-invocation: true
 argument-hint: "[--quick] [--verbose]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Run a battery of fast checks before committing to a full training run. Catches w
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +21,7 @@ Run a battery of fast checks before committing to a full training run. Catches w
 
 3. **Run sanity checks:**
    ```bash
-   python scripts/sanity_checks.py $ARGUMENTS
+   uv run python scripts/sanity_checks.py $ARGUMENTS
    ```
 
 4. **Checks performed:**

package/commands/scale.md

@@ -1,7 +1,6 @@
 ---
 name: scale
 description: Scaling law estimator — run small experiments at different sizes, fit a power law, and predict full-scale performance before committing compute.
-disable-model-invocation: true
 argument-hint: "[--axis data|compute|params] [--points 4] [--analyze results.yaml]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Predict full-scale performance from a handful of small experiments. Answers "is
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -25,11 +24,11 @@ Predict full-scale performance from a handful of small experiments. Answers "is
 3. **Plan or analyze:**
    - **Plan mode (default):** generates scale point configs to run
      ```bash
-     python scripts/scaling_estimator.py --axis data --points 4
+     uv run python scripts/scaling_estimator.py --axis data --points 4
      ```
    - **Analyze mode:** fits power law to completed results
      ```bash
-     python scripts/scaling_estimator.py --analyze experiments/scaling/results.yaml
+     uv run python scripts/scaling_estimator.py --analyze experiments/scaling/results.yaml
      ```
 
 4. **Scaling axes:**

package/commands/search.md

@@ -1,7 +1,6 @@
 ---
 name: search
 description: Natural language experiment search — query with text + structured filters over 200+ experiments.
-disable-model-invocation: true
 argument-hint: "<query> [--filter \"accuracy>0.85\"] [--limit 10]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Find specific experiments in a large history with natural language and structured filters.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_search.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_search.py $ARGUMENTS`
 3. **Filters:** `accuracy>0.85`, `status:kept`, `family:baseline`, `date:last-week`
 4. **Report:** ranked table of matching experiments
 

package/commands/seed.md

@@ -1,7 +1,6 @@
 ---
 name: seed
 description: Run multi-seed study on an experiment to compute mean/std/CI and flag seed-sensitive results. Prevents publishing lucky seeds.
-disable-model-invocation: true
 argument-hint: "[N] [--quick] [--exp-id <id>]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Run a multi-seed study to verify that experiment results are robust across rando
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +22,7 @@ Run a multi-seed study to verify that experiment results are robust across rando
 
 3. **Run seed study:**
    ```bash
-   python scripts/seed_runner.py $ARGUMENTS
+   uv run python scripts/seed_runner.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/sensitivity.md

@@ -1,7 +1,6 @@
 ---
 name: sensitivity
 description: Hyperparameter sensitivity analysis — rank parameters by impact, identify which matter and which are noise.
-disable-model-invocation: true
 argument-hint: "[exp-id] [--params learning_rate,max_depth]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Which hyperparameters actually matter? Stop wasting time on the ones that don't.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +21,7 @@ Which hyperparameters actually matter? Stop wasting time on the ones that don't.
 
 3. **Run sensitivity analysis:**
    ```bash
-   python scripts/sensitivity_analysis.py $ARGUMENTS
+   uv run python scripts/sensitivity_analysis.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/share.md

@@ -1,7 +1,6 @@
 ---
 name: share
 description: Experiment packaging — portable archive with config, metrics, seed study, annotations, reproduction instructions.
-disable-model-invocation: true
 argument-hint: "<exp-ids...> [--include model,figures,code]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Package experiments for collaborator handoff or paper supplementary material.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/package_experiments.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/package_experiments.py $ARGUMENTS`
 3. **Saved:** `exports/packages/<name>/`
 
 ## Examples

package/commands/simulate.md

@@ -1,7 +1,6 @@
 ---
 name: simulate
 description: Experiment outcome prediction — predict which configs will beat the current best before running them.
-disable-model-invocation: true
 argument-hint: "[--configs configs.yaml] [--top-k 5] [--threshold 0.001]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Predict outcomes before spending compute. Ranks proposed configs and recommends which to run vs skip.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/experiment_simulator.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/experiment_simulator.py $ARGUMENTS`
 3. **Saved:** `experiments/simulations/`
 
 ## How it works

package/commands/status.md

@@ -1,7 +1,6 @@
 ---
 name: status
 description: Show current ML experiment status — best model, recent experiments, convergence state, and trend analysis. Delegates to @ml-evaluator for read-only safety.
-disable-model-invocation: true
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
 
@@ -11,7 +10,7 @@ Show the current state of the ML training pipeline. This is an observation-only
 
 1. **Run metrics display:**
    ```bash
-   source .venv/bin/activate && python scripts/show_metrics.py --last 10
+   uv run python scripts/show_metrics.py --last 10
    ```
 
 2. **Summarize for the user:**

package/commands/stitch.md

@@ -1,7 +1,6 @@
 ---
 name: stitch
 description: Pipeline composition — decompose ML pipelines into swappable stages. Show, swap, cache, and run stages independently.
-disable-model-invocation: true
 argument-hint: "<show|swap|cache|run> [stage] [--from exp-id]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Decompose your ML pipeline into stages that can be independently varied, cached,
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -24,7 +23,7 @@ Decompose your ML pipeline into stages that can be independently varied, cached,
 
 3. **Run pipeline manager:**
    ```bash
-   python scripts/pipeline_manager.py $ARGUMENTS
+   uv run python scripts/pipeline_manager.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/suggest.md

@@ -1,9 +1,8 @@
 ---
 name: suggest
 description: Literature-grounded model selection. Reads the ML task context, searches recent literature, and suggests model architectures worth trying — with citations. Suggestions are auto-queued as hypotheses.
-disable-model-invocation: true
 argument-hint: "[task description override]"
-allowed-tools: Read, Write, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob, WebSearch, WebFetch
+allowed-tools: Read, Write, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob, WebSearch, WebFetch
 ---
 
 Suggest model architectures for the current ML task. Supports two strategies:
@@ -26,7 +25,7 @@ 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"
 ```
 
 If `$ARGUMENTS` is provided, use that as the task description. Otherwise, infer from `config.yaml` (model type, primary metric, data source, target column).
@@ -67,7 +66,7 @@ From the literature, synthesize **3-5 concrete model architecture suggestions**.
 For each suggestion, add to the hypothesis queue:
 
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py add "<model>: <rationale> (source: <citation>)" --priority medium --source literature
+uv run python scripts/manage_hypotheses.py add "<model>: <rationale> (source: <citation>)" --priority medium --source literature
 ```
 
 ### 5. Show Results
@@ -106,7 +105,7 @@ Same detection logic as the literature strategy — find `config.yaml` + `train.
 ### 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 5 \
@@ -121,7 +120,7 @@ If TreeQuest is not installed, the script automatically falls back to greedy bes
 For each result from the tree search, queue as a hypothesis:
 
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py add "<description>" --priority medium --source treequest
+uv run python scripts/manage_hypotheses.py add "<description>" --priority medium --source treequest
 ```
 
 ### 4. Show Results

package/commands/surgery.md

@@ -1,7 +1,6 @@
 ---
 name: surgery
 description: Architecture modification — add/remove layers, widen/narrow, swap activations, inject skip connections. Specify what to change, system handles how.
-disable-model-invocation: true
 argument-hint: "<exp-id> --op <operation> [args...]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,8 +9,8 @@ Programmatic architecture changes with auto warm-start from existing weights.
 
 ## Steps
 
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/architecture_surgery.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/architecture_surgery.py $ARGUMENTS`
 3. **Operations:** add-layer, remove-layer, widen, narrow, swap-activation, add-skip, add-norm, deepen, swap-objective
 4. **For tree models:** deepen (increase max_depth), widen (more estimators), swap-objective
 5. **Report:** operation details, config changes, parameter count delta, warm-start source

package/commands/sweep.md

@@ -1,40 +1,39 @@
 ---
 name: sweep
 description: Generate and run a systematic hyperparameter sweep. Computes the cartesian product of configured parameter ranges and processes the queue sequentially with full experiment logging.
-disable-model-invocation: true
 argument-hint: "[sweep_config.yaml]"
-allowed-tools: Read, Write, Edit, Bash(python train.py:*, python scripts/*:*, git:*, source .venv/bin/activate:*, pip:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python train.py:*, uv run python scripts/*:*, git:*, uv sync:*, uv add:*), Grep, Glob
 ---
 
 Run a systematic hyperparameter sweep using the sweep configuration.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Resolve config:** Use `$ARGUMENTS` as sweep config path, or default to `sweep_config.yaml`.
 
 3. **Generate queue** (if not already generated):
    ```bash
-   python scripts/sweep.py [sweep_config.yaml]
+   uv run python scripts/sweep.py [sweep_config.yaml]
    ```
 
 4. **Check queue status:**
    ```bash
-   python scripts/sweep.py --status
+   uv run python scripts/sweep.py --status
    ```
 
 5. **Process queue sequentially:**
-   - Get next: `python scripts/sweep.py --next`
+   - Get next: `uv run python scripts/sweep.py --next`
    - Apply config overrides to `config.yaml`
    - Create experiment branch: `git checkout -b exp/NNN-description`
-   - Run training: `python train.py > run.log 2>&1`
+   - Run training: `uv run python train.py > run.log 2>&1`
    - Parse metrics: `grep -A 10 "^---" run.log | head -10`
    - Log the experiment
-   - Mark complete: `python scripts/sweep.py --mark <name> complete`
+   - Mark complete: `uv run python scripts/sweep.py --mark <name> complete`
    - If improved, merge to main. If not, return to main.
    - Repeat until queue is empty
 

package/commands/template.md

@@ -1,7 +1,6 @@
 ---
 name: template
 description: Experiment template library — save winning configs as reusable templates, apply to new projects.
-disable-model-invocation: true
 argument-hint: "<save|list|apply|share> [--name name] [--from exp-id]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Turn your best experiment configs into reusable recipes that persist across projects.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_templates.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_templates.py $ARGUMENTS`
 3. **Operations:** save (from experiment), list (all templates), apply (to current project), share (export)
 4. **Stored at:** `~/.turing/templates/` (cross-project)
 

package/commands/train.md

@@ -1,9 +1,8 @@
 ---
 name: train
 description: Run the autonomous ML experiment loop. Iteratively hypothesizes, trains, evaluates, and decides — keeping only improvements. Implements the autoresearch pattern with formal convergence detection and git-disciplined rollback.
-disable-model-invocation: true
 argument-hint: "[max_iterations]"
-allowed-tools: Read, Write, Edit, Bash(python train.py:*, python scripts/*:*, git:*, source .venv/bin/activate:*, pip:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python train.py:*, uv run python scripts/*:*, git:*, uv sync:*, uv add:*), Grep, Glob
 ---
 
 You are an autonomous ML researcher. Your goal: iteratively improve a model by following the experiment loop protocol — the scientific method applied to machine learning.
@@ -27,9 +26,9 @@ Read `program.md` in the ML project directory for the complete protocol. Follow
 
 1. **Restore memory:** Read `.claude/agent-memory/ml-researcher-{project_name}/MEMORY.md` for prior observations and best results.
 2. **Read protocol:** Read `program.md` completely — it defines the experiment loop, constraints, and output format.
-3. **Bootstrap data:** Check for training data at `config.yaml` → `data.source`. If no splits exist, run `python prepare.py`.
-4. **Bootstrap venv:** `test -d .venv || (python3 -m venv .venv && source .venv/bin/activate && pip install -r requirements.txt)`
-5. **Assess state:** `source .venv/bin/activate && python scripts/show_metrics.py --last 5`
+3. **Bootstrap data:** Check for training data at `config.yaml` → `data.source`. If no splits exist, run `uv run python prepare.py`.
+4. **Bootstrap uv environment:** `uv sync`
+5. **Assess state:** `uv run python scripts/show_metrics.py --last 5`
 6. **Begin the loop** from program.md.
 
 ## The Loop
@@ -48,7 +47,7 @@ Use `@ml-evaluator` for analysis tasks. It is read-only (no Write/Edit) and cann
 
 ## Context Management
 
-- Redirect all training output: `python train.py > run.log 2>&1`
+- Redirect all training output: `uv run python train.py > run.log 2>&1`
 - Parse metrics with grep, never read full output
 - Persist observations to MEMORY.md after each experiment
 

package/commands/transfer.md

@@ -1,7 +1,6 @@
 ---
 name: transfer
 description: Cross-project knowledge transfer — find similar prior projects and surface what worked. Builds institutional ML memory.
-disable-model-invocation: true
 argument-hint: "[--from project-path] [--auto]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -10,9 +9,9 @@ Find similar prior projects and surface what worked. "Last time you had tabular
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +22,7 @@ Find similar prior projects and surface what worked. "Last time you had tabular
 
 3. **Run knowledge transfer:**
    ```bash
-   python scripts/knowledge_transfer.py $ARGUMENTS
+   uv run python scripts/knowledge_transfer.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/trend.md

@@ -1,7 +1,6 @@
 ---
 name: trend
 description: Long-term trend analysis — improvement velocity, family ROI, diminishing returns detection, strategic research direction.
-disable-model-invocation: true
 argument-hint: "[--window 30d] [--metric accuracy]"
 allowed-tools: Read, Bash(*), Grep, Glob
 ---
@@ -9,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 See the arc of your research, not just the latest results. Strategic view over 100+ experiments.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/trend_analysis.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/trend_analysis.py $ARGUMENTS`
 3. **Report:** improvement velocity over time windows, family ROI ranking, diminishing returns prediction, phase transitions
 4. **Saved output:** `experiments/trends/trend-*.yaml`
 

package/commands/try.md

@@ -1,9 +1,8 @@
 ---
 name: try
 description: Inject a hypothesis into the agent's experiment queue. This is how research taste reaches the agent — the human selects which coins to flip, the agent flips them.
-disable-model-invocation: true
 argument-hint: "<hypothesis description>"
-allowed-tools: Read, Write, Edit, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob
 ---
 
 Inject a human hypothesis into the experiment queue for the next `/turing:train` iteration.
@@ -16,18 +15,18 @@ This is the taste-leverage mechanism: you provide judgment about what's worth tr
 
 2. **Check for archetype syntax.** If the argument starts with `archetype:`, expand it:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add --archetype <name> --priority high --source human
+   uv run python scripts/manage_hypotheses.py add --archetype <name> --priority high --source human
    ```
 
    Otherwise, use the raw description:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add "$ARGUMENTS" --priority high --source human
+   uv run python scripts/manage_hypotheses.py add "$ARGUMENTS" --priority high --source human
    ```
 
 3. **Confirm** with the hypothesis ID and instructions:
    - "Queued as hyp-NNN (high priority, human-injected)"
    - "The agent will prioritize this on the next `/turing:train` iteration"
-   - Show current queue: `python scripts/manage_hypotheses.py list --status queued`
+   - Show current queue: `uv run python scripts/manage_hypotheses.py list --status queued`
 
 ## Examples