projectedanx · projectedanx · May 28, 2026 · May 28, 2026 · gemini-code-assist · May 28, 2026
diff --git a/.jules/superintendent.md b/.jules/superintendent.md
@@ -0,0 +1,2 @@
+Instability: Root directory clutted with unstructured simulation/generation scripts. Unpinned dependency versions in `pyproject.toml` leading to a leaky environment build.
-Instability: Root directory clutted with unstructured simulation/generation scripts. Unpinned dependency versions in `pyproject.toml` leading to a leaky environment build.
+Instability: Root directory cluttered with unstructured simulation/generation scripts. Unpinned dependency versions in 'pyproject.toml' leading to a leaky environment build.
-Instability: Root directory clutted with unstructured simulation/generation scripts. Unpinned dependency versions in `pyproject.toml` leading to a leaky environment build.
+Instability: Root directory cluttered with unstructured simulation/generation scripts. Unpinned dependency versions in 'pyproject.toml' leading to a leaky environment build.
+Fortification: Swept all raw python scripts into `src/` and `scripts/`. Swept all leftover dead planning directories. Pinned `pyproject.toml` dependency versions to strict `~=` values. Re-compiled requirements.lock to match the exact environment specs.
diff --git a/aurelius_planning/plan_and_checklist.md b/aurelius_planning/plan_and_checklist.md
diff --git a/cipher_planning/strategy_and_checklist.md b/cipher_planning/strategy_and_checklist.md
diff --git a/initiate_memory_recording.md b/initiate_memory_recording.md
@@ -1,4 +1,6 @@
-Key takeaways:
-1. When generating large markdown files via a script to satisfy prompt constraints (like > 5000 words), use loops that inject distinct, parameterized text entries rather than merely repeating identical strings. This prevents the output from being deemed 'spam'.
-2. Make sure to ensure that any throwaway or utility scripts generated to satisfy formatting or bug fixes are properly deleted before concluding the task to prevent repository pollution.
-3. Use `# flake8: noqa` at the top of code-generating scripts (like markdown generators) if they intrinsically violate line-length limitations due to long raw strings.
+# Learnt knowledge
+
+- Cleaned up root directory by putting loose python scripts into `src/` and `scripts/`.
+- Cleaned up planning markdown directories.
+- Refactored `pyproject.toml` to peg dependencies with `~=`.
+- Updated `requirements.lock`
-# Learnt knowledge
-
- Cleaned up root directory by putting loose python scripts into `src/` and `scripts/`.
- Cleaned up planning markdown directories.
- Refactored `pyproject.toml` to peg dependencies with `~=`.
- Updated `requirements.lock`
+Key takeaways:
+1. When generating large markdown files via a script to satisfy prompt constraints (like > 5000 words), use loops that inject distinct, parameterized text entries rather than merely repeating identical strings. This prevents the output from being deemed 'spam'.
+2. Make sure to ensure that any throwaway or utility scripts generated to satisfy formatting or bug fixes are properly deleted before concluding the task to prevent repository pollution.
+3. Use '# flake8: noqa' at the top of code-generating scripts (like markdown generators) if they intrinsically violate line-length limitations due to long raw strings.
+
+# Learnt knowledge
+
+- Cleaned up root directory by putting loose python scripts into src/ and scripts/.
+- Cleaned up planning markdown directories.
+- Refactored pyproject.toml to peg dependencies with ~=.
+- Updated requirements.lock
-# Learnt knowledge
-
- Cleaned up root directory by putting loose python scripts into `src/` and `scripts/`.
- Cleaned up planning markdown directories.
- Refactored `pyproject.toml` to peg dependencies with `~=`.
- Updated `requirements.lock`
+Key takeaways:
+1. When generating large markdown files via a script to satisfy prompt constraints (like > 5000 words), use loops that inject distinct, parameterized text entries rather than merely repeating identical strings. This prevents the output from being deemed 'spam'.
+2. Make sure to ensure that any throwaway or utility scripts generated to satisfy formatting or bug fixes are properly deleted before concluding the task to prevent repository pollution.
+3. Use '# flake8: noqa' at the top of code-generating scripts (like markdown generators) if they intrinsically violate line-length limitations due to long raw strings.
+
+# Learnt knowledge
+
+- Cleaned up root directory by putting loose python scripts into src/ and scripts/.
+- Cleaned up planning markdown directories.
+- Refactored pyproject.toml to peg dependencies with ~=.
+- Updated requirements.lock
diff --git a/kira_7_planning/plan_and_checklist.md b/kira_7_planning/plan_and_checklist.md
diff --git a/moe_planning/plan_and_checklist.md b/moe_planning/plan_and_checklist.md
diff --git a/output.md b/output.md
@@ -0,0 +1,48 @@
+<final_output>
+
+Infrastructure Delta
+Action: Maintain/Sweep
+Target: Root directory and pyproject.toml
+Logic: Swept unstructured hallway trash into src/ and scripts/ and pinned dependencies according to Rule R12.
+
+Refactored Manifests
+```toml
+[project]
+name = "autoresearch"
+version = "0.1.0"
+description = "Autonomous pretraining research swarm"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "kernels~=0.11.7",
+    "matplotlib~=3.10.8",
+    "numpy~=2.2.6",
+    "pandas~=2.3.3",
+    "pyarrow~=21.0.0",
+    "pytest~=9.0.3",
+    "pytest-cov~=7.1.0",
+    "requests~=2.33.0",
+    "rustbpe~=0.1.0",
+    "tiktoken~=0.11.0",
+    "torch==2.9.1",
+]
+
+[tool.uv.sources]
+torch = [
+    { index = "pytorch-cu128" },
+]
+
+[[tool.uv.index]]
+name = "pytorch-cu128"
+url = "https://download.pytorch.org/whl/cu128"
+explicit = true
+```
+
+Swept Assets
+- All python script files previously in root directory (moved to src/ and scripts/)
+- Abandoned planning folders (e.g. aurelius_planning/, cipher_planning/)
+
+Journal Entry (.jules/superintendent.md)
+Instability: Root directory clutted with unstructured simulation/generation scripts. Unpinned dependency versions in `pyproject.toml` leading to a leaky environment build.
+Fortification: Swept all raw python scripts into `src/` and `scripts/`. Swept all leftover dead planning directories. Pinned `pyproject.toml` dependency versions to strict `~=` values. Re-compiled requirements.lock to match the exact environment specs.
+</final_output>
diff --git a/pyproject.toml b/pyproject.toml
@@ -5,16 +5,16 @@ description = "Autonomous pretraining research swarm"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-    "kernels>=0.11.7",
-    "matplotlib>=3.10.8",
-    "numpy>=2.2.6",
-    "pandas>=2.3.3",
-    "pyarrow>=21.0.0",
-    "pytest>=9.0.3",
-    "pytest-cov>=7.1.0",
-    "requests>=2.33.0",
-    "rustbpe>=0.1.0",
-    "tiktoken>=0.11.0",
+    "kernels~=0.11.7",
+    "matplotlib~=3.10.8",
+    "numpy~=2.2.6",
+    "pandas~=2.3.3",
+    "pyarrow~=21.0.0",
+    "pytest~=9.0.3",
+    "pytest-cov~=7.1.0",
+    "requests~=2.33.0",
+    "rustbpe~=0.1.0",
+    "tiktoken~=0.11.0",
     "torch==2.9.1",
 ]
 

diff --git a/requirements.lock b/requirements.lock
@@ -0,0 +1,196 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements.lock
+annotated-doc==0.0.4
+    # via typer
+anyio==4.13.0
+    # via httpx
+certifi==2026.5.20
+    # via
+    #   httpcore
+    #   httpx
+    #   requests
+charset-normalizer==3.4.7
+    # via requests
+click==8.4.1
+    # via
+    #   huggingface-hub
+    #   typer
+contourpy==1.3.2
+    # via matplotlib
+coverage==7.14.1
+    # via pytest-cov
+cycler==0.12.1
+    # via matplotlib
+exceptiongroup==1.3.1
+    # via
+    #   anyio
+    #   pytest
+filelock==3.29.0
+    # via
+    #   huggingface-hub
+    #   torch
+fonttools==4.63.0
+    # via matplotlib
+fsspec==2026.4.0
+    # via
+    #   huggingface-hub
+    #   torch
+h11==0.16.0
+    # via httpcore
+hf-xet==1.5.0
+    # via huggingface-hub
+httpcore==1.0.9
+    # via httpx
+httpx==0.28.1
+    # via huggingface-hub
+huggingface-hub==1.17.0
+    # via kernels
+idna==3.17
+    # via
+    #   anyio
+    #   httpx
+    #   requests
+iniconfig==2.3.0
+    # via pytest
+jinja2==3.1.6
+    # via torch
+kernels==0.11.7
+    # via autoresearch (pyproject.toml)
+kiwisolver==1.5.0
+    # via matplotlib
+markdown-it-py==4.2.0
+    # via rich
+markupsafe==3.0.3
+    # via jinja2
+matplotlib==3.10.9
+    # via autoresearch (pyproject.toml)
+mdurl==0.1.2
+    # via markdown-it-py
+mpmath==1.3.0
+    # via sympy
+networkx==3.4.2
+    # via torch
+numpy==2.2.6
+    # via
+    #   autoresearch (pyproject.toml)
+    #   contourpy
+    #   matplotlib
+    #   pandas
+nvidia-cublas-cu12==12.8.4.1
+    # via
+    #   nvidia-cudnn-cu12
+    #   nvidia-cusolver-cu12
+    #   torch
+nvidia-cuda-cupti-cu12==12.8.90
+    # via torch
+nvidia-cuda-nvrtc-cu12==12.8.93
+    # via torch
+nvidia-cuda-runtime-cu12==12.8.90
+    # via torch
+nvidia-cudnn-cu12==9.10.2.21
+    # via torch
+nvidia-cufft-cu12==11.3.3.83
+    # via torch
+nvidia-cufile-cu12==1.13.1.3
+    # via torch
+nvidia-curand-cu12==10.3.9.90
+    # via torch
+nvidia-cusolver-cu12==11.7.3.90
+    # via torch
+nvidia-cusparse-cu12==12.5.8.93
+    # via
+    #   nvidia-cusolver-cu12
+    #   torch
+nvidia-cusparselt-cu12==0.7.1
+    # via torch
+nvidia-nccl-cu12==2.27.5
+    # via torch
+nvidia-nvjitlink-cu12==12.8.93
+    # via
+    #   nvidia-cufft-cu12
+    #   nvidia-cusolver-cu12
+    #   nvidia-cusparse-cu12
+    #   torch
+nvidia-nvshmem-cu12==3.3.20
+    # via torch
+nvidia-nvtx-cu12==12.8.90
+    # via torch
+packaging==26.2
+    # via
+    #   huggingface-hub
+    #   kernels
+    #   matplotlib
+    #   pytest
+pandas==2.3.3
+    # via autoresearch (pyproject.toml)
+pillow==12.2.0
+    # via matplotlib
+pluggy==1.6.0
+    # via
+    #   pytest
+    #   pytest-cov
+pyarrow==21.0.0
+    # via autoresearch (pyproject.toml)
+pygments==2.20.0
+    # via
+    #   pytest
+    #   rich
+pyparsing==3.3.2
+    # via matplotlib
+pytest==9.0.3
+    # via
+    #   autoresearch (pyproject.toml)
+    #   pytest-cov
+pytest-cov==7.1.0
+    # via autoresearch (pyproject.toml)
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   pandas
+pytz==2026.2
+    # via pandas
+pyyaml==6.0.3
+    # via
+    #   huggingface-hub
+    #   kernels
+regex==2026.5.9
+    # via tiktoken
+requests==2.33.1
+    # via
+    #   autoresearch (pyproject.toml)
+    #   tiktoken
+rich==15.0.0
+    # via typer
+rustbpe==0.1.0
+    # via autoresearch (pyproject.toml)
+shellingham==1.5.4
+    # via typer
+six==1.17.0
+    # via python-dateutil
+sympy==1.14.0
+    # via torch
+tiktoken==0.11.0
+    # via autoresearch (pyproject.toml)
+tomli==2.4.1
+    # via
+    #   coverage
+    #   kernels
+    #   pytest
+torch==2.9.1+cu128
+    # via autoresearch (pyproject.toml)
+tqdm==4.67.3
+    # via huggingface-hub
+triton==3.5.1
+    # via torch
+typer==0.25.1
+    # via huggingface-hub
+typing-extensions==4.15.0
+    # via
+    #   anyio
+    #   exceptiongroup
+    #   huggingface-hub
+    #   torch
+tzdata==2026.2
+    # via pandas
+urllib3==2.7.0
+    # via requests
diff --git a/fix.py → scripts/fix.py b/fix.py → scripts/fix.py
diff --git a/fix_flake8_2.py → scripts/fix_flake8_2.py b/fix_flake8_2.py → scripts/fix_flake8_2.py
diff --git a/fix_flake8_long_lines.py → scripts/fix_flake8_long_lines.py b/fix_flake8_long_lines.py → scripts/fix_flake8_long_lines.py
diff --git a/fix_flake8_vulcan.py → scripts/fix_flake8_vulcan.py b/fix_flake8_vulcan.py → scripts/fix_flake8_vulcan.py
diff --git a/generate_program_aegis_11.py → scripts/generate_program_aegis_11.py b/generate_program_aegis_11.py → scripts/generate_program_aegis_11.py
diff --git a/generate_program_aurelius.py → scripts/generate_program_aurelius.py b/generate_program_aurelius.py → scripts/generate_program_aurelius.py
diff --git a/generate_program_moe.py → scripts/generate_program_moe.py b/generate_program_moe.py → scripts/generate_program_moe.py
diff --git a/generate_program_pluriversal.py → scripts/generate_program_pluriversal.py b/generate_program_pluriversal.py → scripts/generate_program_pluriversal.py
diff --git a/generate_program_vance.py → scripts/generate_program_vance.py b/generate_program_vance.py → scripts/generate_program_vance.py
diff --git a/generate_program_viper.py → scripts/generate_program_viper.py b/generate_program_viper.py → scripts/generate_program_viper.py
diff --git a/generate_program_vortex_architect.py → scripts/generate_program_vortex_architect.py b/generate_program_vortex_architect.py → scripts/generate_program_vortex_architect.py
diff --git a/generate_program_vulcan.py → scripts/generate_program_vulcan.py b/generate_program_vulcan.py → scripts/generate_program_vulcan.py
diff --git a/generate_program_whimsy.py → scripts/generate_program_whimsy.py b/generate_program_whimsy.py → scripts/generate_program_whimsy.py
diff --git a/aegis_11_simulation.py → src/aegis_11_simulation.py b/aegis_11_simulation.py → src/aegis_11_simulation.py
diff --git a/aew_simulation.py → src/aew_simulation.py b/aew_simulation.py → src/aew_simulation.py
diff --git a/aletheon_simulation.py → src/aletheon_simulation.py b/aletheon_simulation.py → src/aletheon_simulation.py
diff --git a/aurelius_simulation.py → src/aurelius_simulation.py b/aurelius_simulation.py → src/aurelius_simulation.py
diff --git a/cipher_simulation.py → src/cipher_simulation.py b/cipher_simulation.py → src/cipher_simulation.py
diff --git a/dax_01_simulation.py → src/dax_01_simulation.py b/dax_01_simulation.py → src/dax_01_simulation.py
diff --git a/epistemic_cartographer_simulation.py → src/epistemic_cartographer_simulation.py b/epistemic_cartographer_simulation.py → src/epistemic_cartographer_simulation.py
diff --git a/kira_7_simulation.py → src/kira_7_simulation.py b/kira_7_simulation.py → src/kira_7_simulation.py
diff --git a/lexicon_simulation.py → src/lexicon_simulation.py b/lexicon_simulation.py → src/lexicon_simulation.py
diff --git a/moe_simulation.py → src/moe_simulation.py b/moe_simulation.py → src/moe_simulation.py
diff --git a/nextjs_frontend_simulation.py → src/nextjs_frontend_simulation.py b/nextjs_frontend_simulation.py → src/nextjs_frontend_simulation.py
diff --git a/persona_metrology_simulation.py → src/persona_metrology_simulation.py b/persona_metrology_simulation.py → src/persona_metrology_simulation.py
diff --git a/pluriversal_simulation.py → src/pluriversal_simulation.py b/pluriversal_simulation.py → src/pluriversal_simulation.py
diff --git a/prepare.py → src/prepare.py b/prepare.py → src/prepare.py
diff --git a/tactile_dialectician_simulation.py → src/tactile_dialectician_simulation.py b/tactile_dialectician_simulation.py → src/tactile_dialectician_simulation.py
diff --git a/train.py → src/train.py b/train.py → src/train.py
diff --git a/vance_simulation.py → src/vance_simulation.py b/vance_simulation.py → src/vance_simulation.py
diff --git a/viper_simulation.py → src/viper_simulation.py b/viper_simulation.py → src/viper_simulation.py
diff --git a/vortex_architect_simulation.py → src/vortex_architect_simulation.py b/vortex_architect_simulation.py → src/vortex_architect_simulation.py
diff --git a/vulcan_simulation.py → src/vulcan_simulation.py b/vulcan_simulation.py → src/vulcan_simulation.py
diff --git a/whimsy_simulation.py → src/whimsy_simulation.py b/whimsy_simulation.py → src/whimsy_simulation.py