initial dir structure

.gitignore

@@ -1,207 +1,24 @@
-# Byte-compiled / optimized / DLL files
+# Python
 __pycache__/
-*.py[codz]
+*.py[cod]
 *$py.class
-
-# C extensions
 *.so
-
-# Distribution / packaging
 .Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py.cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# UV
-#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#uv.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-#poetry.toml
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
-#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
-#pdm.lock
-#pdm.toml
-.pdm-python
-.pdm-build/
-
-# pixi
-#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
-#pixi.lock
-#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
-#   in the .venv directory. It is recommended not to include this directory in version control.
-.pixi
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.envrc
-.venv
 env/
 venv/
+.venv/
 ENV/
-env.bak/
-venv.bak/
 
-# Spyder project settings
-.spyderproject
-.spyproject
+# Secrets & config
+agentserver/config/organism_identity/private.pem
+agentserver/config/*.signed.xml
 
-# Rope project settings
-.ropeproject
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
 
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-
-# Abstra
-# Abstra is an AI-powered process automation framework.
-# Ignore directories containing user credentials, local state, and settings.
-# Learn more at https://abstra.io/docs
-.abstra/
-
-# Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
-#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
-#  you could uncomment the following to ignore the entire vscode folder
-# .vscode/
-
-# Ruff stuff:
-.ruff_cache/
-
-# PyPI configuration file
-.pypirc
-
-# Cursor
-#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
-#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
-#  refer to https://docs.cursor.com/context/ignore-files
-.cursorignore
-.cursorindexingignore
-
-# Marimo
-marimo/_static/
-marimo/_lsp/
-__marimo__/
+# OS
+Thumbs.db
+.DS_Store

agentserver/config/organism_identity/README.txt

@@ -0,0 +1,2 @@
+Place your permanent Ed25519 private.pem and public.pem here.
+Private key must be tightly guarded - never commit it.

scripts/generate_organism_key.py

@@ -0,0 +1,2 @@
+# One-time tool to generate the permanent Ed25519 organism identity
+# Run once, store private key offline/safely

setup-project.ps1

@@ -0,0 +1,93 @@
+# setup-project.ps1
+# Run this from the root of your AgentServer repo to create the full directory structure
+
+Write-Host "Creating AgentServer project structure..." -ForegroundColor Green
+
+# Main package and core files
+New-Item -ItemType Directory -Force -Path "agentserver" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\main.py"
+New-Item -ItemType File -Force -Path "agentserver\agentserver.py"
+New-Item -ItemType File -Force -Path "agentserver\message_bus.py"
+New-Item -ItemType File -Force -Path "agentserver\llm_connection.py"
+
+# Privileged commands
+New-Item -ItemType Directory -Force -Path "agentserver\privileged" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\privileged\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\privileged\commands.py"
+
+# Authentication
+New-Item -ItemType Directory -Force -Path "agentserver\auth" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\auth\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\auth\totp.py"
+
+# Agents
+New-Item -ItemType Directory -Force -Path "agentserver\agents" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\agents\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\agents\base.py"
+
+New-Item -ItemType Directory -Force -Path "agentserver\agents\examples" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\agents\examples\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\agents\examples\echo_chamber.py"
+
+# Config
+New-Item -ItemType Directory -Force -Path "agentserver\config" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\config\__init__.py"
+
+New-Item -ItemType Directory -Force -Path "agentserver\config\organism_identity" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\config\organism_identity\README.txt" -Value "Place your permanent Ed25519 private.pem and public.pem here.`nPrivate key must be tightly guarded - never commit it."
+
+New-Item -ItemType File -Force -Path "agentserver\config\initial_config.signed.xml" -Value "<!-- Signed boot-time configuration (LLM pools, initial agents, etc.) will go here -->"
+
+# Utils
+New-Item -ItemType Directory -Force -Path "agentserver\utils" | Out-Null
+New-Item -ItemType File -Force -Path "agentserver\utils\__init__.py"
+New-Item -ItemType File -Force -Path "agentserver\utils\xml_tools.py"
+New-Item -ItemType File -Force -Path "agentserver\utils\logging_setup.py"
+
+# Top-level supporting folders
+New-Item -ItemType Directory -Force -Path "tests" | Out-Null
+New-Item -ItemType File -Force -Path "tests\__init__.py"
+
+New-Item -ItemType Directory -Force -Path "scripts" | Out-Null
+New-Item -ItemType File -Force -Path "scripts\generate_organism_key.py" -Value "# One-time tool to generate the permanent Ed25519 organism identity`n# Run once, store private key offline/safely"
+
+# .gitignore
+$gitignoreContent = @'
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+.venv/
+ENV/
+
+# Secrets & config
+agentserver/config/organism_identity/private.pem
+agentserver/config/*.signed.xml
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+Thumbs.db
+.DS_Store
+'@
+
+Set-Content -Path ".gitignore" -Value $gitignoreContent
+
+Write-Host "Directory structure created successfully!" -ForegroundColor Green
+Write-Host ""
+Write-Host "Next steps:" -ForegroundColor Cyan
+Write-Host "1. git add ."
+Write-Host "2. git commit -m 'chore: initial project skeleton with modular structure'"
+Write-Host "3. git push"
+Write-Host "4. In PyCharm: right-click 'agentserver' folder -> Mark Directory as -> Sources Root"
+Write-Host ""
+Write-Host "The organism now has its full skeletal system. Ready to breathe."