├── .clinerules ├── .dockerignore ├── .env.example ├── .github ├── FUNDING.yml └── workflows │ └── publish.yml ├── .gitignore ├── .ncurc.json ├── .repomixignore ├── CHANGELOG.md ├── CLAUDE.md ├── LICENSE ├── README.md ├── automated-tests └── AGENT_TEST_05282025.md ├── docker-compose.yml ├── docs └── tree.md ├── examples ├── README.md ├── backup-example │ ├── knowledges.json │ ├── projects.json │ ├── relationships.json │ └── tasks.json ├── deep-research-example │ ├── covington_community_grant_research.md │ └── full-export.json └── webui-example.png ├── mcp.json ├── package.json ├── repomix.config.json ├── scripts ├── clean.ts ├── fetch-openapi-spec.ts ├── make-executable.ts └── tree.ts ├── smithery.yaml ├── src ├── config │ └── index.ts ├── index.ts ├── mcp │ ├── resources │ │ ├── index.ts │ │ ├── knowledge │ │ │ └── knowledgeResources.ts │ │ ├── projects │ │ │ └── projectResources.ts │ │ ├── tasks │ │ │ └── taskResources.ts │ │ └── types.ts │ ├── server.ts │ ├── tools │ │ ├── atlas_database_clean │ │ │ ├── cleanDatabase.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_deep_research │ │ │ ├── deepResearch.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_knowledge_add │ │ │ ├── addKnowledge.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_knowledge_delete │ │ │ ├── deleteKnowledge.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_knowledge_list │ │ │ ├── index.ts │ │ │ ├── listKnowledge.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_project_create │ │ │ ├── createProject.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_project_delete │ │ │ ├── deleteProject.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_project_list │ │ │ ├── index.ts │ │ │ ├── listProjects.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_project_update │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ ├── types.ts │ │ │ └── updateProject.ts │ │ ├── atlas_task_create │ │ │ ├── createTask.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_task_delete │ │ │ ├── deleteTask.ts │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_task_list │ │ │ ├── index.ts │ │ │ ├── listTasks.ts │ │ │ ├── responseFormat.ts │ │ │ └── types.ts │ │ ├── atlas_task_update │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ ├── types.ts │ │ │ └── updateTask.ts │ │ └── atlas_unified_search │ │ │ ├── index.ts │ │ │ ├── responseFormat.ts │ │ │ ├── types.ts │ │ │ └── unifiedSearch.ts │ └── transports │ │ ├── authentication │ │ └── authMiddleware.ts │ │ ├── httpTransport.ts │ │ └── stdioTransport.ts ├── services │ └── neo4j │ │ ├── backupRestoreService │ │ ├── backupRestoreTypes.ts │ │ ├── backupUtils.ts │ │ ├── exportLogic.ts │ │ ├── importLogic.ts │ │ ├── index.ts │ │ └── scripts │ │ │ ├── db-backup.ts │ │ │ └── db-import.ts │ │ ├── driver.ts │ │ ├── events.ts │ │ ├── helpers.ts │ │ ├── index.ts │ │ ├── knowledgeService.ts │ │ ├── projectService.ts │ │ ├── searchService │ │ ├── fullTextSearchLogic.ts │ │ ├── index.ts │ │ ├── searchTypes.ts │ │ └── unifiedSearchLogic.ts │ │ ├── taskService.ts │ │ ├── types.ts │ │ └── utils.ts ├── types │ ├── errors.ts │ ├── mcp.ts │ └── tool.ts ├── utils │ ├── index.ts │ ├── internal │ │ ├── errorHandler.ts │ │ ├── index.ts │ │ ├── logger.ts │ │ └── requestContext.ts │ ├── metrics │ │ ├── index.ts │ │ └── tokenCounter.ts │ ├── parsing │ │ ├── dateParser.ts │ │ ├── index.ts │ │ └── jsonParser.ts │ └── security │ │ ├── idGenerator.ts │ │ ├── index.ts │ │ ├── rateLimiter.ts │ │ └── sanitization.ts └── webui │ ├── index.html │ ├── logic │ ├── api-service.js │ ├── app-state.js │ ├── config.js │ ├── dom-elements.js │ ├── main.js │ └── ui-service.js │ └── styling │ ├── base.css │ ├── components.css │ ├── layout.css │ └── theme.css ├── tsconfig.json ├── 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