jordan 41c676a78e feat: Aphoria enterprise features + ontology SDK + file length compliance

Enterprise Features:
- Hosted mode with remote sync for team pattern aggregation
- Community sharing with privacy-preserving anonymization
- LLM-based semantic claim extraction with Gemini integration
- Pattern learning with promotion to declarative extractors
- High-entropy secrets extractor with configurable thresholds
- Auth bypass and insecure cookies extractors

Module Refactoring:
- Split oversized files to comply with 500-line limit
- Config split: types/core.rs, types/extractors.rs, types/hosted.rs, etc.
- Handlers split: scan.rs, policy.rs, report.rs modules
- Extractors split: declarative/, high_entropy_secrets/, insecure_cookies/
- Learning split: store modules with metrics and persistence

SDK & Ontology:
- stemedb-ontology SDK with fluent builders and StemeDB client
- Pharma domain extractors for FDA Orange Book data
- Consumer health UAT test infrastructure

Code Quality:
- Fixed clippy warnings (needless_borrows_for_generic_args)
- Added KVStore trait imports where needed
- Fixed utoipa path re-exports for OpenAPI docs

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2026-02-05 12:55:29 -07:00

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Aphoria Configuration

Last Updated: 2026-02-04 Confidence: High

Summary

Aphoria uses aphoria.toml for project-level configuration. Two key sections handle where observations are stored: [episteme] for local storage and [hosted] for team server sync. When [hosted].url is set, observations automatically sync to the team's StemeDB server.

Key Facts:

Config file: aphoria.toml at project root
Local storage: [episteme].data_dir (default: ~/.aphoria/db)
Hosted mode: [hosted].url enables team aggregation
Sync is implicit when hosted mode is configured (no --sync needed)
sync_mode: remote-only (default) or local-and-remote

File Pointer: applications/aphoria/src/config.rs:1-400

Configuration Sections

Project Identity

[project]
name = "my-service"     # Auto-detected if not set
language = "rust"       # Auto-detected if not set

Local Storage (`[episteme]`)

[episteme]
data_dir = "~/.aphoria/db"    # Local Episteme storage
url = "http://localhost:18180" # Remote Episteme (future)

File Pointer: applications/aphoria/src/config.rs:68-83

Hosted Mode (`[hosted]`)

Enables team-wide observation aggregation:

[hosted]
url = "https://episteme.acme.corp"  # Enables hosted mode
project_id = "billing-service"       # Defaults to [project.name]
team_id = "platform-team"            # Optional, for multi-team servers
sync_mode = "remote-only"            # "remote-only" | "local-and-remote"
offline_fallback = "skip"            # "skip" | "fail" | "queue"
api_key_env = "APHORIA_API_KEY"      # Env var for auth token
max_retries = 3                      # HTTP retry attempts
retry_delay_ms = 1000                # Delay between retries

File Pointer: applications/aphoria/src/config.rs:298-380

Sync Mode Options

Mode	Local Storage	Remote Push	Use Case
`remote-only`	No	Yes	Teams want single source of truth
`local-and-remote`	Yes	Yes	Need local history + team sync

Offline Fallback Options

Mode	Behavior	Use Case
`skip`	Warn and continue	Don't block developers
`fail`	Error and abort	CI/CD mandatory sync
`queue`	Queue for later (not implemented)	Future offline support

Server Endpoint

Hosted clients POST to /v1/aphoria/observations:

File Pointer: crates/stemedb-api/src/handlers/aphoria.rs:340-430

Aphoria Roadmap - Phase 4E details
API Surface - HTTP API reference

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