LICENSE
README.md
pyproject.toml
setup.cfg
setup.py
bin/fermilink-optimize-cpp
bin/fermilink-optimize-python
src/fermilink/__init__.py
src/fermilink/__main__.py
src/fermilink/agent_runtime.py
src/fermilink/config.py
src/fermilink/providers.py
src/fermilink/router_rules.py
src/fermilink/services.py
src/fermilink.egg-info/PKG-INFO
src/fermilink.egg-info/SOURCES.txt
src/fermilink.egg-info/dependency_links.txt
src/fermilink.egg-info/entry_points.txt
src/fermilink.egg-info/requires.txt
src/fermilink.egg-info/top_level.txt
src/fermilink/agents/__init__.py
src/fermilink/agents/base.py
src/fermilink/agents/claude_agent.py
src/fermilink/agents/codex_agent.py
src/fermilink/agents/deepseek_agent.py
src/fermilink/agents/gemini_agent.py
src/fermilink/agents/registry.py
src/fermilink/cli/__init__.py
src/fermilink/cli/__main__.py
src/fermilink/cli/compile_helpers.py
src/fermilink/cli/compile_prompts.py
src/fermilink/cli/exec_runtime.py
src/fermilink/cli/input_repo_helpers.py
src/fermilink/cli/overlay_helpers.py
src/fermilink/cli/parser_agent.py
src/fermilink/cli/parser_builder.py
src/fermilink/cli/parser_gateway.py
src/fermilink/cli/parser_implement.py
src/fermilink/cli/parser_optimize.py
src/fermilink/cli/parser_packages.py
src/fermilink/cli/parser_services.py
src/fermilink/cli/parser_sessions.py
src/fermilink/cli/parser_workflows.py
src/fermilink/cli/parser_workspace.py
src/fermilink/cli/routing_helpers.py
src/fermilink/cli/runtime_loaders.py
src/fermilink/cli/shared_helpers.py
src/fermilink/cli/workflow_prompts.py
src/fermilink/cli/zero_arg.py
src/fermilink/cli/commands/__init__.py
src/fermilink/cli/commands/agent.py
src/fermilink/cli/commands/gateway.py
src/fermilink/cli/commands/implement.py
src/fermilink/cli/commands/optimize.py
src/fermilink/cli/commands/packages.py
src/fermilink/cli/commands/services.py
src/fermilink/cli/commands/sessions.py
src/fermilink/cli/commands/workflows.py
src/fermilink/cli/commands/workspace.py
src/fermilink/data/curated_channels/skilled-scipkg.json
src/fermilink/data/router/family_hints.json
src/fermilink/data/schemas/curated-channel.v2.schema.json
src/fermilink/data/schemas/family-hints.v2.schema.json
src/fermilink/exploop/AGENTS.md
src/fermilink/exploop/__init__.py
src/fermilink/exploop/artifacts.py
src/fermilink/exploop/instructions.py
src/fermilink/exploop/main.py
src/fermilink/exploop/memory.py
src/fermilink/exploop/pid.py
src/fermilink/exploop/prompts.py
src/fermilink/implement/__init__.py
src/fermilink/implement/campaign.py
src/fermilink/implement/contract.py
src/fermilink/implement/git.py
src/fermilink/implement/goal.py
src/fermilink/implement/main.py
src/fermilink/implement/prompts.py
src/fermilink/implement/source_analysis.py
src/fermilink/implement/state.py
src/fermilink/implement/validation.py
src/fermilink/optimize/__init__.py
src/fermilink/optimize/benchmark.py
src/fermilink/optimize/campaign.py
src/fermilink/optimize/git.py
src/fermilink/optimize/goal.py
src/fermilink/optimize/goal_pipeline.py
src/fermilink/optimize/main.py
src/fermilink/optimize/prompts.py
src/fermilink/optimize/source_analysis.py
src/fermilink/optimize/state.py
src/fermilink/packages/__init__.py
src/fermilink/packages/curated_channels.py
src/fermilink/packages/package_core.py
src/fermilink/packages/package_registry.py
src/fermilink/public/README.md
src/fermilink/public/custom.css
src/fermilink/public/custom.js
src/fermilink/public/fermilink.md
src/fermilink/public/fermilink_logo.png
src/fermilink/public/fermilink_mini_bright.svg
src/fermilink/public/fermilink_mini_dark.svg
src/fermilink/public/fermilink_wordmark.svg
src/fermilink/public/mark.svg
src/fermilink/runner/__init__.py
src/fermilink/runner/admission.py
src/fermilink/runner/app.py
src/fermilink/runner/scientific_packages.py
src/fermilink/software/AGENTS.md
src/fermilink/tools/sci-skills-generator/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-core/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-core/references/driver_quickref.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-core/references/solver_quickref.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-core/scripts/validate_skills_structure.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-ase/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-lammps/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-psi4-rtehrenfest/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-psi4-rttddft/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-qutip/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-driver-tls/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-hpc-slurm/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-hpc-slurm/references/slurm_recipes.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-hpc-slurm/resources/hpc_setting.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-index/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-laser-driven/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-laser-driven/references/laser_run_recipes.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-meep/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-meep/references/meep_run_recipes.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-postprocess/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-postprocess/references/postprocessing.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/laser-tls-embedded/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/laser-tls-embedded/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/laser-tls-embedded/em.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/laser-tls-embedded/run_local.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-embedded/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-embedded/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-embedded/em.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-embedded/run_local.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/driver.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/em.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/run_driver.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/meep-tls-socket-unix/run_em.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/singlemode-tls-socket-tcp/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/singlemode-tls-socket-tcp/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/singlemode-tls-socket-tcp/driver.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/singlemode-tls-socket-tcp/em.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/clean.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/data.lmp
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/em_main.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/in_mxl.lmp
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/lammps_driver.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/submit_all.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/submit_lammps.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-lammps-tcp/submit_main.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/clean.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/driver.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/em_main.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/submit_all.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/submit_driver.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/submit_main.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/HCN_benchmark/frequency_calc.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-plasmon-rteh-tcp/HCN_benchmark/hcn.xyz
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/README.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/clean.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/config.json
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/driver.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/em_main.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/submit_all.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/submit_driver.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/assets/templates/slurm-meep-tls-tcp/submit_main.sh
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/scripts/mxl_scaffold_project.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-project-scaffold/scripts/mxl_validate_project.py
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-singlemode/SKILL.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-singlemode/references/singlemode_run_recipes.md
src/fermilink/tools/sci-skills-generator/assets/maxwelllink-skills-template/skills/mxl-troubleshoot/SKILL.md
src/fermilink/tools/sci-skills-generator/references/example-invocations.md
src/fermilink/tools/sci-skills-generator/references/generation-rubric.md
src/fermilink/tools/sci-skills-generator/scripts/generate_skills_folder.py
src/fermilink/web/__init__.py
src/fermilink/web/activity_helpers.py
src/fermilink/web/app.py
src/fermilink/web/artifact_helpers.py
src/fermilink/web/auth_helpers.py
src/fermilink/web/chat_helpers.py
src/fermilink/web/package_router_helpers.py
src/fermilink/web/package_session_helpers.py
src/fermilink/web/runner_helpers.py
src/fermilink/web/sqlite_helpers.py
src/fermilink/web/status_helpers.py
src/fermilink/web/storage_helpers.py
src/fermilink/workspace/__init__.py
src/fermilink/workspace/clean.py
src/fermilink/workspace/common.py
src/fermilink/workspace/filesystem.py
src/fermilink/workspace/hpc.py
src/fermilink/workspace/init.py
src/fermilink/workspace/main.py
src/fermilink/workspace/payload.py
tests/test_agent_runtime.py
tests/test_agents.py
tests/test_bin_optimize_cpp.py
tests/test_bin_optimize_python.py
tests/test_cli.py
tests/test_cli_agent.py
tests/test_cli_auto_compile.py
tests/test_cli_avail.py
tests/test_cli_bootstrap.py
tests/test_cli_chat.py
tests/test_cli_compile.py
tests/test_cli_exec.py
tests/test_cli_gateway.py
tests/test_cli_implement.py
tests/test_cli_init_clean.py
tests/test_cli_loop.py
tests/test_cli_optimize.py
tests/test_cli_optimize_goal.py
tests/test_cli_recompile.py
tests/test_cli_reproduce.py
tests/test_cli_research.py
tests/test_cli_services.py
tests/test_cli_services_live.py
tests/test_cli_summary_output.py
tests/test_config.py
tests/test_curated_channels.py
tests/test_data_validation.py
tests/test_docs_built_in_scientific_packages.py
tests/test_exploop_mode.py
tests/test_implement_mode.py
tests/test_optimize_package_migration.py
tests/test_optimize_report.py
tests/test_package_registry.py
tests/test_package_registry_compat.py
tests/test_package_registry_zip.py
tests/test_project_optimization_add_entry.py
tests/test_providers.py
tests/test_publish_workflow.py
tests/test_router_rules.py
tests/test_runner_admission.py
tests/test_runner_overlay_manifest.py
tests/test_runner_policy.py
tests/test_runner_run_cleanup.py
tests/test_services.py
tests/test_setup_workspace_payload.py
tests/test_web_app_logs.py
tests/test_web_app_router.py
tests/test_web_auth_signup.py
tests/test_web_chat_helpers.py
tests/test_web_package_session_helpers.py
tests/test_web_runner_integration.py
tests/test_workflow_data_audit_v2.py
tests/test_workspace_package_migration.py