feat(serena): add Serena project config + Agno agent for Cosmos demo

- .serena/project.yml: register FactoryLM as Serena project with language servers
- .gitignore: exclude .serena/memories/ (local-only)
- agents/serena_agent.py: Agno-powered web UI agent using Claude
- scripts/start_serena_agent.sh: launch script for agent + Doppler secrets

On other machines: `claude plugin install serena` to enable MCP tools.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: Mikecranesync

.gitignore

@@ -102,3 +102,6 @@ _BUILDS/cosmos-demo-2026-02-05/
 # Manual backup folders
 scripts/openclaw/restore-feb8/
 _BUILDS/
+
+# Serena memories (local)
+.serena/memories/

.serena/project.yml

@@ -1,124 +1,61 @@
 # the name by which the project can be referenced within Serena
-project_name: "factorylm-monorepo"
+project_name: "factorylm"
 
 
-# list of languages for which language servers are started; choose from:
-#   al                  bash                clojure             cpp                 csharp
-#   csharp_omnisharp    dart                elixir              elm                 erlang
-#   fortran             fsharp              go                  groovy              haskell
-#   java                julia               kotlin              lua                 markdown
-#   matlab              nix                 pascal              perl                php
-#   php_phpactor        powershell          python              python_jedi         r
-#   rego                ruby                ruby_solargraph     rust                scala
-#   swift               terraform           toml                typescript          typescript_vts
-#   vue                 yaml                zig
-#   (This list may be outdated. For the current list, see values of Language enum here:
-#   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py
-#   For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
-# Note:
-#   - For C, use cpp
-#   - For JavaScript, use typescript
-#   - For Free Pascal/Lazarus, use pascal
-# Special requirements:
-#   Some languages require additional setup/installations.
-#   See here for details: https://oraios.github.io/serena/01-about/020_programming-languages.html#language-servers
-# When using multiple languages, the first language server that supports a given file will be used for that file.
-# The first language is the default language and the respective language server will be used as a fallback.
-# Note that when using the JetBrains backend, language servers are not used and this list is correspondingly ignored.
+# list of languages for which language servers are started
 languages:
-- java
+- python
+- typescript
 
 # the encoding used by text files in the project
-# For a list of possible encodings, see https://docs.python.org/3.11/library/codecs.html#standard-encodings
-encoding: "utf-8"
+encoding: utf-8
 
 # whether to use project's .gitignore files to ignore files
 ignore_all_files_in_gitignore: true
 
 # list of additional paths to ignore in this project.
-# Same syntax as gitignore, so you can use * and **.
-# Note: global ignored_paths from serena_config.yml are also applied additively.
-ignored_paths: []
+ignored_paths:
+- "node_modules/**"
+- "_BUILDS/**"
+- "output/**"
+- "Io_sim_images/**"
+- "traces/**"
+- "my-ralph/**"
+- "recordings/**"
+- "test_images/**"
+- "video/**"
+- ".claude/**"
+- "docs/archive/**"
 
 # whether the project is in read-only mode
-# If set to true, all editing tools will be disabled and attempts to use them will result in an error
-# Added on 2025-04-18
 read_only: false
 
-# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
-# Below is the complete list of tools for convenience.
-# To make sure you have the latest list of tools, and to view their descriptions, 
-# execute `uv run scripts/print_tool_overview.py`.
-#
-#  * `activate_project`: Activates a project by name.
-#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
-#  * `create_text_file`: Creates/overwrites a file in the project directory.
-#  * `delete_lines`: Deletes a range of lines within a file.
-#  * `delete_memory`: Deletes a memory from Serena's project-specific memory store.
-#  * `execute_shell_command`: Executes a shell command.
-#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
-#  * `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
-#  * `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filtered by type).
-#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
-#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
-#  * `initial_instructions`: Gets the initial instructions for the current project.
-#     Should only be used in settings where the system prompt cannot be set,
-#     e.g. in clients you have no control over, like Claude Desktop.
-#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
-#  * `insert_at_line`: Inserts content at a given line in a file.
-#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
-#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
-#  * `list_memories`: Lists memories in Serena's project-specific memory store.
-#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
-#  * `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
-#  * `read_file`: Reads a file within the project directory.
-#  * `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
-#  * `remove_project`: Removes a project from the Serena configuration.
-#  * `replace_lines`: Replaces a range of lines within a file with new content.
-#  * `replace_symbol_body`: Replaces the full definition of a symbol.
-#  * `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
-#  * `search_for_pattern`: Performs a search for a pattern in the project.
-#  * `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
-#  * `switch_modes`: Activates modes by providing a list of their names
-#  * `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
-#  * `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
-#  * `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
-#  * `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.
+# list of tool names to exclude.
 excluded_tools: []
 
-# list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default)
+# list of tools to include that would otherwise be disabled
 included_optional_tools: []
 
-# fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
-# This cannot be combined with non-empty excluded_tools or included_optional_tools.
+# fixed set of tools to use as the base tool set
 fixed_tools: []
 
+# initial prompt for the project.
+initial_prompt: >
+  FactoryLM monorepo — industrial AI platform diagnosing factory faults
+  using NVIDIA Cosmos Reason 2. Key dirs: cosmos/ (client, watcher, agent),
+  services/matrix/ (FastAPI + SQLite), diagnosis/ (conveyor fault rules),
+  sim/ (PLC simulator + Factory I/O bridge), core/ (shared Python library).
+  Pipeline: Factory I/O -> Modbus TCP -> Matrix API -> Cosmos -> Diagnosis.
+  SAFETY: NEVER modify code tagged # SAFETY, # PLC, or # CRITICAL.
+
 # list of mode names to that are always to be included in the set of active modes
-# The full set of modes to be activated is base_modes + default_modes.
-# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply.
-# Otherwise, this setting overrides the global configuration.
-# Set this to [] to disable base modes for this project.
-# Set this to a list of mode names to always include the respective modes for this project.
 base_modes:
 
 # list of mode names that are to be activated by default.
-# The full set of modes to be activated is base_modes + default_modes.
-# If the setting is undefined, the default_modes from the global configuration (serena_config.yml) apply.
-# Otherwise, this overrides the setting from the global configuration (serena_config.yml).
-# This setting can, in turn, be overridden by CLI parameters (--mode).
 default_modes:
 
-# initial prompt for the project. It will always be given to the LLM upon activating the project
-# (contrary to the memories, which are loaded on demand).
-initial_prompt: ""
-
-# override of the corresponding setting in serena_config.yml, see the documentation there.
-# If null or missing, the value from the global config is used.
+# time budget (seconds) per tool call for the retrieval of additional symbol information
 symbol_info_budget:
 
 # The language backend to use for this project.
-# If not set, the global setting from serena_config.yml is used.
-# Valid values: LSP, JetBrains
-# Note: the backend is fixed at startup. If a project with a different backend
-# is activated post-init, an error will be returned.
 language_backend:

agents/serena_agent.py

@@ -0,0 +1,37 @@
+"""FactoryLM Serena Agent — Agno-powered web UI for codebase navigation.
+
+Launch via: doppler run -p factorylm -c dev -- uv run python agents/serena_agent.py --project .
+Requires: serena[agno] installed in Desktop/serena venv.
+UI: connect Agent UI at http://localhost:3000 to http://localhost:7777
+"""
+import sys
+from pathlib import Path
+
+# Add the serena source to path so we can import it
+SERENA_ROOT = Path(__file__).resolve().parent.parent.parent / "serena"
+if SERENA_ROOT.exists():
+    sys.path.insert(0, str(SERENA_ROOT / "src"))
+
+from agno.models.anthropic.claude import Claude
+from agno.os import AgentOS
+from sensai.util import logging as sensai_logging
+
+from serena.agno import SerenaAgnoAgentProvider
+
+if __name__ == "__main__":
+    sensai_logging.configure(level=sensai_logging.INFO)
+
+model = Claude(id="claude-sonnet-4-20250514")
+
+serena_agent = SerenaAgnoAgentProvider.get_agent(model)
+
+agent_os = AgentOS(
+    description="FactoryLM coding assistant — industrial AI codebase navigation",
+    id="factorylm-serena",
+    agents=[serena_agent],
+)
+
+app = agent_os.get_app()
+
+if __name__ == "__main__":
+    agent_os.serve(app="serena_agent:app", reload=False)

scripts/start_serena_agent.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# Start the FactoryLM Serena Agent with Agno web UI
+# Requires: serena[agno] installed in ~/Desktop/serena/.venv
+# UI: connect Agent UI at http://localhost:3000 to http://localhost:7777
+
+SERENA_ROOT="C:/Users/hharp/OneDrive/Desktop/serena"
+FACTORYLM_ROOT="C:/Users/hharp/OneDrive/Desktop/FactoryLM"
+
+cd "$SERENA_ROOT" || exit 1
+
+export SERENA_ROOT
+
+doppler run -p factorylm -c dev -- \
+  uv run python "$FACTORYLM_ROOT/agents/serena_agent.py" \
+  --project "$FACTORYLM_ROOT"