name	yams
description	Code indexing, exact/semantic search, graph-assisted code navigation, and project memory
license	GPL-3.0
compatibility	opencode
metadata	{"tools":"cli, mcp","categories":"search, indexing, memory, knowledge-graph"}

YAMS Skill (agent.md)

Quick Reference

# Status & Health
yams status                    # Check daemon and index status
yams daemon start              # Start background daemon
yams doctor                    # Diagnose issues

# Indexing
yams add <file>                # Index single file
yams add . -r --include "*.py" # Index directory recursively
yams watch                     # Auto-index on file changes

# Search (use grep first, search for semantic)
yams grep "pattern" --cwd .    # Code pattern search scoped to current project
yams grep -e "--flag" --cwd .  # Explicit pattern for leading '-' text
yams grep -g "*.cpp" "TODO"   # rg-style glob filtering
yams grep --minimal "TODO"     # Compact grep-style output
yams search "query"            # Semantic/hybrid search

# Graph
yams graph --explore <query>   # Agent context: symbols, relationships, snippets
yams graph --name <file>       # Raw file relationships
yams graph --list-types        # List node types with counts
yams graph --relations         # List relation types with counts
yams graph --search "pattern"  # Search nodes by label
# graph owns path/tree/topology inspection; retired tree is not top-level

# Agent storage
yams list --format json        # Scriptable list output
yams list --show-metadata      # Include metadata for work item

Agent Memory Workflow

YAMS is the single source of truth for agent memory and work item.

Required Metadata (Task Tracking)

Attach metadata to every yams add.

task - short task slug (e.g., list-json-refresh)
phase - start | checkpoint | complete
owner - agent or author
source - code | note | decision | research

Index Project Files

# Index specific file types
yams add . -r --include "*.ts,*.tsx,*.js"

# Index with exclusions
yams add . -r --include "*.py" --exclude "venv/**,__pycache__/**"

# Index with metadata for tracking
yams add src/ -r --metadata "task=list-json-refresh,phase=checkpoint,owner=codex,source=code"

Auto-Index with Watch

yams watch                     # Start watching current directory
yams watch --interval 2000     # Custom interval (ms)
yams watch --stop              # Stop watching

Verify Indexing

yams status                    # Shows indexed file count
yams list --limit 10           # Recent indexed files

Search Patterns

Decision Tree

Code patterns → yams grep (fast, regex/literal; use --cwd . for repo scoping)
Semantic/concept → yams search (embeddings/hybrid)
Codebase shape / blast radius → yams graph --explore from a search/grep hit
Path/tree/topology inspection → use yams graph, not retired top-level tree
No results from grep → Try yams search, then follow graph_explore_hint when present

grep (Code Search)

# Exact pattern
yams grep "function authenticate"

# Regex pattern
yams grep "async.*await.*fetch"

# With context lines
yams grep "TODO" -A 2 -B 2

# Filter by extension
yams grep "import" --ext py

# rg-style glob filter (repeatable)
yams grep -g "src/**/*.cpp" "TODO"

# Compact grep-style output (default is richer agent context)
yams grep --minimal "TODO" -g "src/**/*.cpp"

# Scope to current working directory or an explicit directory
yams grep "TODO" --cwd .
yams grep "TODO" --cwd src/daemon

# Literal text (no regex)
yams grep "user?.name" -F

# Per-file match cap: --limit is an alias for -m/--max-count, not global
# Use search/list --limit for global result caps.
yams grep "TODO" -m 5

# Pattern starts with '-': use -- or explicit -e/--regexp
yams grep -- "--tags|foo" --include="docs/**/*.md"
yams grep --regexp "--tags|foo" -g "docs/**/*.md"

search (Semantic Search)

# Concept search
yams search "error handling patterns"

# Hybrid search (default)
yams search "authentication flow" --type hybrid

# Limit results
yams search "database connection" --limit 5

# Filter by file type
yams search "API endpoint" --ext ts

search (Metadata-Only)

# Force metadata/FTS path for structured metadata
yams search "task=example-task" --type keyword --limit 10

# Unique task selection (avoid collisions)
yams search "task=example-task" --type keyword --limit 20
# 2) List all used task values with counts

# Tag filters (tags are stored as metadata keys: tag:<name>)
yams search "plan" --type keyword --tags plan --limit 10
yams search "tagged logic" --type keyword --tags plan --limit 20

Agent Storage

Store Research

# Index documentation
curl -s "https://docs.example.com/api" | yams add - --name "api-docs.md" \
  --metadata "task=docs-cache,phase=checkpoint,owner=codex,source=research"

# Store with metadata
yams add notes.md --metadata "task=research-auth,phase=checkpoint,owner=codex,source=research"

Store Decisions

# Pipe decision record
echo "## Decision: Use JWT for auth

### Context
Need stateless authentication for microservices.

### Decision
JWT with RS256, 15min expiry, refresh tokens.

### Rationale
Stateless, scalable, industry standard.
" | yams add - --name "decision-jwt-auth.md" \
  --metadata "task=auth-decision,phase=checkpoint,owner=codex,source=decision"

Retrieve Knowledge

# Find related decisions
yams search "authentication decision"

# Find by metadata (JSON list is the source of truth)
yams list --format json --show-metadata \
  | jq '.documents[] | select(.metadata.task=="example-task")'

# Metadata + tags are separate in JSON output
yams list --format json --show-metadata \
  | jq '.documents[] | {name,metadata,tags}'

Session Management

Create Work Sessions

# Start named session
yams session start --name "feature-auth"

# List sessions
yams session ls

# Switch session
yams session use "feature-auth"

# Show current session
yams session show --json

Session Scope

# Add files to session scope
yams session add --path "src/auth/**"

# Warm session cache (faster searches)
yams session warm --limit 100

# Search within session
yams search "login" --session

Session Lifecycle

# Save session state
yams session save

# Load previous session
yams session load --name "feature-auth"

# Clear session cache
yams session clear

# End session
yams session close

Graph Queries

Use graph after search/grep finds a likely entry point. Graph answers "what is connected to this?" and should guide local reads, not replace them.

Agent Graph Context

# Preferred follow-up after search/grep hints: ranked symbols + line-numbered snippets
yams graph --explore "authenticateUser" --max-files 3

# Explore a file path when the result path is more useful than a symbol name
yams graph --explore src/auth/login.ts --max-files 8

# JSON for tool consumers
yams graph --explore "RequestHandler" --json

Notes:

yams search and yams grep results may emit graph_explore_hint; run that exact command before broad local search.
--explore is budgeted for agents: entry symbols, related files, relationship summaries, and line-numbered snippets.
If --explore fails or looks stale, fall back to raw traversal plus local reads.

Raw Graph Structure

# List available node types and relation types
yams graph --list-types
yams graph --relations

# Search nodes by label pattern (wildcards: * any chars, ? single char)
yams graph --search "*Controller*"
yams graph --search "auth*"
yams graph --search "handle?Request"

# List scoped node types
yams graph --list-type function --scope-cwd --limit 50

File / Symbol Relationships

# Show file dependencies and symbols
yams graph --name src/auth/login.ts --depth 2 --limit 50

# Filter by relation type when doing blast-radius review
yams graph --name src/main.ts --relation includes --depth 1
yams graph --node-key "func:authenticate" --relation calls --depth 2

# Output as JSON or DOT
yams graph --name src/auth/login.ts --format json
yams graph --name src/auth/login.ts --format dot > graph.dot

Common relations: calls, includes, contains, defined_in, located_in, has_version, semantic_neighbor.

Topology Navigation

# Find subsystem clusters and their medoid/bridge/core files
yams graph --topology-snapshots
yams graph --topology-clusters
yams graph --cluster <cluster-id>

Use topology when entering an unfamiliar subsystem. Start with medoids for representative files, bridges for cross-subsystem coupling, and core files for local implementation detail.

MCP Integration

YAMS exposes tools via Model Context Protocol for programmatic access.

Start MCP Server

yams serve                     # Start MCP server (quiet mode)
yams serve --verbose           # With logging

Available MCP Tools (Code Mode)

The MCP server exposes a small composite tool surface.

Tool	Purpose
`query`	Read-only pipeline: `search`, `grep`, `list`, `list_collections`, `list_snapshots`, `graph`, `get`, `status`, `describe`
`execute`	Write batch: `add`, `update`, `delete`, `restore`, `download`
`session`	Session lifecycle: `start`, `stop`, `pin`, `unpin`, `watch` (extensions enabled)
`mcp.echo`	Echo utility

Notes:

query and execute accept arrays (steps / operations) and run them in order.
Each query.steps[i] result is available to later steps via $prev (e.g., $prev.results[0].hash).
Use describe to discover the parameter schema for an operation at runtime.

Example (pipeline: search -> get):

{
  "name": "query",
  "arguments": {
    "steps": [
      {"op": "search", "params": {"query": "auth middleware", "limit": 1}},
      {"op": "get", "params": {"hash": "$prev.results[0].hash", "include_content": true}}
    ]
  }
}

MCP Configuration

{
  "mcpServers": {
    "yams": {
      "command": "yams",
      "args": ["serve"]
    }
  }
}

MCP Environment Toggles

Variable	Effect
`YAMS_DISABLE_EXTENSIONS=1`	Disable YAMS extensions (removes `session`, disables some methods like `logging/setLevel`)
`YAMS_DAEMON_SOCKET=/path.sock`	Override daemon socket path used by MCP server

Troubleshooting

# Check daemon status
yams daemon status -d

# View daemon logs
yams daemon log -n 50

# Full diagnostic
yams doctor

# Repair index
yams doctor repair --all

# Fix embedding dimensions
yams doctor --fix-config-dims

Environment Variables

Variable	Purpose
`YAMS_DATA_DIR`	Storage directory
`YAMS_DAEMON_SOCKET`	Daemon socket path override
`YAMS_LOG_LEVEL`	Logging verbosity
`YAMS_SESSION_CURRENT`	Default session
docs/skills/yams/SKILL.md

name	yams
description	Code indexing, exact/semantic search, graph-assisted code navigation, and project memory
license	GPL-3.0
compatibility	opencode
metadata	{"tools":"cli, mcp","categories":"search, indexing, memory, knowledge-graph"}

YAMS Skill (agent.md)

Quick Reference

# Status & Health
yams status                    # Check daemon and index status
yams daemon start              # Start background daemon
yams doctor                    # Diagnose issues

# Indexing
yams add <file>                # Index single file
yams add . -r --include "*.py" # Index directory recursively
yams watch                     # Auto-index on file changes

# Search (use grep first, search for semantic)
yams grep "pattern" --cwd .    # Code pattern search scoped to current project
yams grep -e "--flag" --cwd .  # Explicit pattern for leading '-' text
yams grep -g "*.cpp" "TODO"   # rg-style glob filtering
yams grep --minimal "TODO"     # Compact grep-style output
yams search "query"            # Semantic/hybrid search

# Graph
yams graph --explore <query>   # Agent context: symbols, relationships, snippets
yams graph --name <file>       # Raw file relationships
yams graph --list-types        # List node types with counts
yams graph --relations         # List relation types with counts
yams graph --search "pattern"  # Search nodes by label
# graph owns path/tree/topology inspection; retired tree is not top-level

# Agent storage
yams list --format json        # Scriptable list output
yams list --show-metadata      # Include metadata for work item

Agent Memory Workflow

YAMS is the single source of truth for agent memory and work item.

Required Metadata (Task Tracking)

Attach metadata to every yams add.

task - short task slug (e.g., list-json-refresh)
phase - start | checkpoint | complete
owner - agent or author
source - code | note | decision | research

Index Project Files

# Index specific file types
yams add . -r --include "*.ts,*.tsx,*.js"

# Index with exclusions
yams add . -r --include "*.py" --exclude "venv/**,__pycache__/**"

# Index with metadata for tracking
yams add src/ -r --metadata "task=list-json-refresh,phase=checkpoint,owner=codex,source=code"

Auto-Index with Watch

yams watch                     # Start watching current directory
yams watch --interval 2000     # Custom interval (ms)
yams watch --stop              # Stop watching

Verify Indexing

yams status                    # Shows indexed file count
yams list --limit 10           # Recent indexed files

Search Patterns

Decision Tree

Code patterns → yams grep (fast, regex/literal; use --cwd . for repo scoping)
Semantic/concept → yams search (embeddings/hybrid)
Codebase shape / blast radius → yams graph --explore from a search/grep hit
Path/tree/topology inspection → use yams graph, not retired top-level tree
No results from grep → Try yams search, then follow graph_explore_hint when present

grep (Code Search)

# Exact pattern
yams grep "function authenticate"

# Regex pattern
yams grep "async.*await.*fetch"

# With context lines
yams grep "TODO" -A 2 -B 2

# Filter by extension
yams grep "import" --ext py

# rg-style glob filter (repeatable)
yams grep -g "src/**/*.cpp" "TODO"

# Compact grep-style output (default is richer agent context)
yams grep --minimal "TODO" -g "src/**/*.cpp"

# Scope to current working directory or an explicit directory
yams grep "TODO" --cwd .
yams grep "TODO" --cwd src/daemon

# Literal text (no regex)
yams grep "user?.name" -F

# Per-file match cap: --limit is an alias for -m/--max-count, not global
# Use search/list --limit for global result caps.
yams grep "TODO" -m 5

# Pattern starts with '-': use -- or explicit -e/--regexp
yams grep -- "--tags|foo" --include="docs/**/*.md"
yams grep --regexp "--tags|foo" -g "docs/**/*.md"

search (Semantic Search)

# Concept search
yams search "error handling patterns"

# Hybrid search (default)
yams search "authentication flow" --type hybrid

# Limit results
yams search "database connection" --limit 5

# Filter by file type
yams search "API endpoint" --ext ts

search (Metadata-Only)

# Force metadata/FTS path for structured metadata
yams search "task=example-task" --type keyword --limit 10

# Unique task selection (avoid collisions)
yams search "task=example-task" --type keyword --limit 20
# 2) List all used task values with counts

# Tag filters (tags are stored as metadata keys: tag:<name>)
yams search "plan" --type keyword --tags plan --limit 10
yams search "tagged logic" --type keyword --tags plan --limit 20

Agent Storage

Store Research

# Index documentation
curl -s "https://docs.example.com/api" | yams add - --name "api-docs.md" \
  --metadata "task=docs-cache,phase=checkpoint,owner=codex,source=research"

# Store with metadata
yams add notes.md --metadata "task=research-auth,phase=checkpoint,owner=codex,source=research"

Store Decisions

# Pipe decision record
echo "## Decision: Use JWT for auth

### Context
Need stateless authentication for microservices.

### Decision
JWT with RS256, 15min expiry, refresh tokens.

### Rationale
Stateless, scalable, industry standard.
" | yams add - --name "decision-jwt-auth.md" \
  --metadata "task=auth-decision,phase=checkpoint,owner=codex,source=decision"

Retrieve Knowledge

# Find related decisions
yams search "authentication decision"

# Find by metadata (JSON list is the source of truth)
yams list --format json --show-metadata \
  | jq '.documents[] | select(.metadata.task=="example-task")'

# Metadata + tags are separate in JSON output
yams list --format json --show-metadata \
  | jq '.documents[] | {name,metadata,tags}'

Session Management

Create Work Sessions

# Start named session
yams session start --name "feature-auth"

# List sessions
yams session ls

# Switch session
yams session use "feature-auth"

# Show current session
yams session show --json

Session Scope

# Add files to session scope
yams session add --path "src/auth/**"

# Warm session cache (faster searches)
yams session warm --limit 100

# Search within session
yams search "login" --session

Session Lifecycle

# Save session state
yams session save

# Load previous session
yams session load --name "feature-auth"

# Clear session cache
yams session clear

# End session
yams session close

Graph Queries

Use graph after search/grep finds a likely entry point. Graph answers "what is connected to this?" and should guide local reads, not replace them.

Agent Graph Context

# Preferred follow-up after search/grep hints: ranked symbols + line-numbered snippets
yams graph --explore "authenticateUser" --max-files 3

# Explore a file path when the result path is more useful than a symbol name
yams graph --explore src/auth/login.ts --max-files 8

# JSON for tool consumers
yams graph --explore "RequestHandler" --json

Notes:

yams search and yams grep results may emit graph_explore_hint; run that exact command before broad local search.
--explore is budgeted for agents: entry symbols, related files, relationship summaries, and line-numbered snippets.
If --explore fails or looks stale, fall back to raw traversal plus local reads.

Raw Graph Structure

# List available node types and relation types
yams graph --list-types
yams graph --relations

# Search nodes by label pattern (wildcards: * any chars, ? single char)
yams graph --search "*Controller*"
yams graph --search "auth*"
yams graph --search "handle?Request"

# List scoped node types
yams graph --list-type function --scope-cwd --limit 50

File / Symbol Relationships

# Show file dependencies and symbols
yams graph --name src/auth/login.ts --depth 2 --limit 50

# Filter by relation type when doing blast-radius review
yams graph --name src/main.ts --relation includes --depth 1
yams graph --node-key "func:authenticate" --relation calls --depth 2

# Output as JSON or DOT
yams graph --name src/auth/login.ts --format json
yams graph --name src/auth/login.ts --format dot > graph.dot

Common relations: calls, includes, contains, defined_in, located_in, has_version, semantic_neighbor.

Topology Navigation

# Find subsystem clusters and their medoid/bridge/core files
yams graph --topology-snapshots
yams graph --topology-clusters
yams graph --cluster <cluster-id>

Use topology when entering an unfamiliar subsystem. Start with medoids for representative files, bridges for cross-subsystem coupling, and core files for local implementation detail.

MCP Integration

YAMS exposes tools via Model Context Protocol for programmatic access.

Start MCP Server

yams serve                     # Start MCP server (quiet mode)
yams serve --verbose           # With logging

Available MCP Tools (Code Mode)

The MCP server exposes a small composite tool surface.

Tool	Purpose
`query`	Read-only pipeline: `search`, `grep`, `list`, `list_collections`, `list_snapshots`, `graph`, `get`, `status`, `describe`
`execute`	Write batch: `add`, `update`, `delete`, `restore`, `download`
`session`	Session lifecycle: `start`, `stop`, `pin`, `unpin`, `watch` (extensions enabled)
`mcp.echo`	Echo utility

Notes:

query and execute accept arrays (steps / operations) and run them in order.
Each query.steps[i] result is available to later steps via $prev (e.g., $prev.results[0].hash).
Use describe to discover the parameter schema for an operation at runtime.

Example (pipeline: search -> get):

{
  "name": "query",
  "arguments": {
    "steps": [
      {"op": "search", "params": {"query": "auth middleware", "limit": 1}},
      {"op": "get", "params": {"hash": "$prev.results[0].hash", "include_content": true}}
    ]
  }
}

MCP Configuration

{
  "mcpServers": {
    "yams": {
      "command": "yams",
      "args": ["serve"]
    }
  }
}

MCP Environment Toggles

Variable	Effect
`YAMS_DISABLE_EXTENSIONS=1`	Disable YAMS extensions (removes `session`, disables some methods like `logging/setLevel`)
`YAMS_DAEMON_SOCKET=/path.sock`	Override daemon socket path used by MCP server

Troubleshooting

# Check daemon status
yams daemon status -d

# View daemon logs
yams daemon log -n 50

# Full diagnostic
yams doctor

# Repair index
yams doctor repair --all

# Fix embedding dimensions
yams doctor --fix-config-dims

Environment Variables

Variable	Purpose
`YAMS_DATA_DIR`	Storage directory
`YAMS_DAEMON_SOCKET`	Daemon socket path override
`YAMS_LOG_LEVEL`	Logging verbosity
`YAMS_SESSION_CURRENT`	Default session
docs/skills/yams/SKILL.md