Configuration

Project DNA

SYNAPSEED uses a cascading configuration system called DNA (Dynamic Navigation Architecture). Configuration is loaded with the following priority:

1. Project-level — .synapseed/dna.yaml (highest priority)
2. User-level — ~/.config/synapseed/dna.yaml
3. Embedded defaults (lowest priority)

Configuration File

Create .synapseed/dna.yaml in your project root:

# Workspace layout strategy
workspace_strategy: monorepo

# Preferred libraries for architecture guidance
preferred_libs:
  async: tokio
  json: serde_json
  error: thiserror
  cli: clap
  http: reqwest

# Naming conventions
naming:
  core_crate: core
  bin_name: synapseed

# Enabled plugins
plugins:
  - cortex
  - husk
  - root
  - chronos

# DLP sensitivity level
dlp_level: standard

# Custom DLP rules
dlp_custom_rules:
  - name: internal_id
    pattern: 'INTERNAL-\d{6}'
    action: redact

# DLP false-positive whitelist (regex patterns)
dlp_whitelist:
  - CancellationToken
  - test_secret_\w+

# Search index settings
search:
  persistence: true
  embeddings: true
  temporal_decay_lambda: 0.01

# Context configuration (Whisper symbol pruning)
context:
  max_symbols: 5

# HCI (Human-Computer Interaction) settings
hci:
  background_indexing: true
  port_retry: true
  adaptive_linting: true
  mentor_mode: true
  session_persistence: true
  memory_ceiling_files: 10000
  model_profile: null  # "atomic", "molecular", or "galactic"

# Code security pattern scanning
security_patterns:
  enabled: true
  categories: []  # empty = all active

# Architect settings

Fields Reference

workspace_strategy

Strategy for workspace layout. Used by the architect tool to provide guidance.

• monorepo — Single repository with multiple crates (default)
• polyrepo — Multiple repositories

preferred_libs

A key-value map of technology categories to preferred libraries. The consult MCP tool uses this to guide the LLM.

naming

• core_crate — Name of the core/shared crate
• bin_name — Name of the main binary

plugins

List of enabled plugins. Available plugins:

Plugin	Description
cortex	AST parsing & code graph
husk	DLP & secret scanning
root	Command sentinel
chronos	Git history analysis

dlp_level

Controls how aggressively the DLP engine scans content.

Level	Behavior
off	No scanning
low	Only high-confidence patterns (AWS keys, private keys)
standard	Default — all patterns including generic secrets
strict	Standard + extended patterns
paranoid	Everything, including heuristic detection

dlp_custom_rules

A list of custom DLP rules merged with built-in defaults.

Field	Type	Description
name	string	Human-readable rule name
pattern	string	Regex or literal pattern to match
action	string	redact, deny, audit, or allow

dlp_whitelist

A list of regex patterns to suppress false-positive DLP findings. If a finding's matched text contains any whitelist pattern, it is ignored.

Example: "CancellationToken" suppresses generic_secret hits on Rust concurrency types.

search

Settings for the semantic search index.

Field	Type	Default	Description
persistence	boolean	false	Persist the Tantivy index to disk at .synapseed/index/
embeddings	boolean	false	Enable vector embedding similarity search. Downloads ~22MB model on first use to .synapseed/models/. Required for the similar tool.
temporal_decay_lambda	float	0.01	Decay rate for temporal search boost. Higher values = stronger recency preference. Score formula: bm25 × (0.7 + 0.3 × e^(−λ × age_days)).

context

Controls how many symbols the Whisper intent router includes in responses.

Field	Type	Default	Description
max_symbols	integer	5	Maximum symbols to include in context. Lower values reduce noise for ultra-small models (<3B).

hci

Human-Computer Interaction settings. Controls perceptual quality features.

Field	Type	Default	Description
background_indexing	boolean	true	Enable non-blocking code indexing at startup
port_retry	boolean	true	Enable automatic port retry for the telemetry gRPC server
adaptive_linting	boolean	true	Enable debounce escalation during rapid edits
mentor_mode	boolean	true	Response depth adapts to query complexity
session_persistence	boolean	true	Enable cross-session continuity
memory_ceiling_files	integer	null	Max files to index (memory ceiling). null = unlimited (default: 10000)
model_profile	string	null	Cognitive profile override: "atomic", "molecular", or "galactic". Overrides auto-detected tier from MCP client fingerprinting.

security_patterns

Controls which vulnerability categories are checked by the scan tool's code pattern scanner.

Field	Type	Default	Description
enabled	boolean	true	Enable code pattern scanning
categories	list	[]	Active categories: sql_injection, xss, command_injection, path_traversal. Empty = all active.

architect

Settings for the architecture analysis engine.

Field	Type	Default	Description
density_high_threshold	float	0.5	Topological density above this triggers a "high density" warning
density_low_threshold	float	0.02	Topological density below this (with ≥ density_low_min_modules modules) triggers a "low density" warning
density_low_min_modules	integer	10	Minimum module count before low-density warnings apply
god_object_max_symbols	integer	50	Max public symbols before flagging as god object
god_object_max_lines	integer	1000	Max approximate lines before flagging as god object
god_object_min_fan_in	integer	5	Min fan-in to combine with size for god object detection
layers	list	[]	Layer definitions for violation detection. Each entry has name, rank, and modules.

Environment Variables

Variable	Default	Description
RUST_LOG	info	Log level filter (trace/debug/info/warn/error)
SYNAPSEED_LOG_FORMAT	compact	Set to json for machine-readable logs
SYNAPSEED_SELF_TELEMETRY	(unset)	Set to 1 to enable self-instrumentation