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YAMS CLI Reference

A practical, task-focused reference for the yams command-line interface.

This document covers global flags, environment variables, and each subcommand with usage notes and examples. It is structured so tools can extract command-specific sections.

For help: - yams --help - Show all available commands - yams <command> --help - Show command-specific help

Synopsis

yams [OPTIONS] <command> [command-options]

Environment Variables

Precedence: configuration file > environment variables > CLI flags

  • YAMS_STORAGE - Storage root directory (overrides --data-dir unless config specifies otherwise)
  • XDG_DATA_HOME - Default storage location (~/.local/share if unset)
  • XDG_CONFIG_HOME - Default config location (~/.config if unset)
  • HOME - Fallback when XDG paths are not set

Global Options

  • --data-dir, --storage <path> - Override storage root (default: $XDG_DATA_HOME/yams)
  • --json - Output in JSON format where supported
  • -v, --verbose - Enable verbose output
  • --version - Display program version
  • -h, --help - Print help message

Commands

Core Operations

  • init - Initialize YAMS storage and configuration
  • add - Add document(s) or directory to content store
  • get - Retrieve a document from content store
  • cat - Display document content to stdout
  • delete, rm - Delete documents by hash, name, or pattern
  • list, ls - List stored documents
  • update - Update metadata for existing document

Search & Discovery

  • search - Search documents by query (semantic + keyword)
  • grep - Search for regex patterns within file contents
  • tree - Inspect aggregated path tree statistics
  • graph - Inspect knowledge graph relationships

Collections & Snapshots

  • restore - Restore documents from collections/snapshots to filesystem
  • diff - Compare two snapshots and show file changes

System Management

  • daemon - Manage YAMS daemon process (start/stop/restart/status)
  • doctor - Diagnose system health, connectivity, and repair issues
  • status - Show quick system status and health overview
  • stats - Show detailed system statistics
  • config - Manage YAMS configuration settings
  • auth - Manage authentication keys and tokens

Advanced Features

  • model - Download and manage ONNX embedding models
  • plugin, plugins - Manage plugins (list/scan/load/unload/trust)
  • session - Manage interactive session pins and warming
  • download - Download artifacts and store directly into YAMS
  • repair - Repair and maintain storage integrity
  • migrate - Migrate YAMS data and configuration
  • dr - Disaster recovery operations (plugin-gated)

User Interface

  • serve - Start MCP (Model Context Protocol) server
  • completion - Generate shell completion scripts (bash/zsh/fish/powershell)

Utilities

  • uninstall - Remove YAMS from your system

init {#cmd-init}

Initialize YAMS storage and configuration (interactive or non-interactive).

Synopsis: - yams init [OPTIONS] [path]

Options: - –non-interactive - Run without prompts, using defaults and passed flags. - –auto - Auto-initialize with all defaults for containerized/headless environments (enables vector DB, plugins, default model; skips S3). - –force - Overwrite existing config/keys if already initialized. - –no-keygen - Skip authentication key generation. - –print - Print resulting configuration to stdout (secrets masked). - –enable-plugins - Create and trust a local plugins directory (~/.local/lib/yams/plugins).

Notes: - The storage directory can be set globally via –storage/–data-dir or YAMS_STORAGE. - On first run, initialization will create the storage directory, database, and configuration. - Interactive mode prompts for tree-sitter grammar downloads for symbol extraction.

Examples: 

# Interactive initialization (prompts for grammar downloads)
yams init .

# Auto mode for containers/headless (downloads recommended grammars)
yams init --auto

# Non-interactive with explicit storage
yams --storage "$HOME/.local/share/yams" init --non-interactive

# Force re-initialization
yams init --force

# Print config without secrets
yams init --print

add {#cmd-add}

Pre-watch code indexing (recommended) Use YAMS to index code updates until folder track/watch is available.

Examples: 

# Index entire source tree (initial import)
yams add src/ --recursive --include="*.cpp,*.hpp,*.h" --tags "code,source"
yams add include/ --recursive --include="*.hpp,*.h" --tags "code,headers"

# Re-index after local edits (quick pass)
yams add . --recursive --include="*.cpp,*.hpp,*.h,*.md" --tags "code,working"

# Add a single updated file
yams add path/to/file.cpp --tags "code,source"

# Update metadata for an existing document by name
yams update --name path/to/file.cpp --metadata "updated=$(date -Iseconds)"

Tips: - Prefer comma-separated patterns with –include for multiple file types. - Tag code consistently (e.g., code,source; code,headers) to improve later queries.

Add a document to the store from a file or stdin.

Synopsis: - yams add [options] - yams add [options] - yams add - [options] # read from stdin

Options: - -n, –name - Set the document name (especially useful for stdin input) - -t, –tags - Comma-separated tags for the document (repeatable) - -m, –metadata - Custom metadata key-value pairs (repeatable) - –mime-type - Override MIME type detection - –no-auto-mime - Disable automatic MIME type detection - –no-embeddings - Disable automatic embedding generation for added documents - -r, –recursive - Recursively add files from directories - –include - File patterns to include (e.g., ‘.txt,.md’) - –exclude - File patterns to exclude (e.g., ‘.tmp,.log’) - -c, –collection - Collection name for organizing documents - –snapshot-id - Unique snapshot identifier - –snapshot-label

Description: - Ingests the specified file or standard input and stores it in the content-addressed store. - Rich metadata support for tagging, naming, and custom properties. - Content is automatically indexed for full-text and fuzzy search. - Automatic snapshots (PBI-043): Every yams add operation automatically creates a snapshot with a timestamp-based ID (e.g., 2025-10-01T14:30:00.123Z). A Merkle tree is built and stored for efficient diff operations. - Trees enable fast yams diff operations using O(log n) subtree matching. - Git integration: When run in a git repository, snapshot metadata includes the current commit hash and branch name.

Examples: 

# Basic document addition (automatic snapshot created)
yams add ./README.md
# → Snapshot: 2025-10-01T14:30:00.123Z

# Add with human-friendly label
yams add . --recursive --label "Release 1.0"
# → Snapshot: 2025-10-01T14:30:00.456Z (label: "Release 1.0")

# Organize by collection
yams add docs/ --recursive --collection=documentation
# → Snapshot: 2025-10-01T14:30:01.789Z (collection: "documentation")

# Standard operations (all create automatic snapshots)
cat notes.txt | yams add - --name "meeting-notes" --tags "work,meeting"
yams add document.pdf --tags "research,papers" --metadata "author=John Doe"
yams add src/ --recursive --include="*.cpp,*.h" --tags "code,source"

Automatic Snapshot Workflows:

  1. Initial import (automatic snapshot): 

    yams add . --recursive --include="*.cpp,*.h,*.md" --label "Initial import"
# → Snapshot: 2025-10-01T09:00:00.000Z

  2. After making changes (automatic snapshot): 

    yams add . --recursive --include="*.cpp,*.h,*.md" --label "Added new feature"
# → Snapshot: 2025-10-01T14:30:00.000Z

  3. Compare any two snapshots: 

    # List all snapshots to find IDs
yams list --snapshots

# Compare using timestamp IDs
yams diff 2025-10-01T09:00:00.000Z 2025-10-01T14:30:00.000Z

  4. View snapshot timeline: 

    yams list --snapshots
# Shows chronological list of all automatic snapshots

Performance Notes: - Tree building adds ~5-10% overhead to yams add but enables O(log n) diff operations. - Trees are stored once in CAS and deduplicated across snapshots. - For large repositories (>10K files), tree-based diff is 10-100x faster than flat comparison. - Automatic snapshots have zero mental overhead - just use yams add normally.

get {#cmd-get}

Retrieve a document by hash or name for downloading.

Synopsis: - yams get [options] - yams get –name [options]

Options: - –name - Retrieve document by name instead of hash - -o, –output - Write output to specified file instead of stdout - -v, –verbose - Enable verbose output - –graph - Show related documents from knowledge graph - –depth - Depth of graph traversal, 1-5 (default: 1)

Description: - Downloads content by hash or name. - For viewing content directly, use the cat command instead. - Supports both stdout redirection and explicit output file specification.

Examples: 

yams get abcd1234... -o output.txt
yams get --name "document.pdf" -o restored.pdf
yams get --name "config.json" > config.json
yams get abcd1234... --verbose

graph {#cmd-graph}

Show related documents via the knowledge graph for a given document (read-only).

Synopsis: - yams graph [–depth N] - yams graph –name [–depth N]

Options: - –name - Resolve the target by path/name instead of hash - –depth - Depth of graph traversal, 1-5 (default: 1) - -v, –verbose - Verbose header details

Description: - Mirrors the graph view available in get --graph without fetching content. - Uses the same daemon request path; shows related documents and their relationship/distance.

Examples: 

yams graph 0123abcd... --depth 2
yams graph --name "docs/readme.md" --depth 3

cat {#cmd-cat}

Display document content to stdout.

Synopsis: - yams cat - yams cat –name

Options: - –name - Display document by name instead of hash

Description: - Outputs content directly to stdout for viewing or piping. - Silent operation - no status messages (ideal for piping). - Use get command for downloading files.

Examples: 

yams cat abcd1234...
yams cat --name "notes.txt"
yams cat --name "config.json" | jq .
yams cat --name "script.sh" | bash

delete {#cmd-delete}

rm {#cmd-rm}

Delete documents by hash, name, or pattern. (Alias: rm)

Synopsis: - yams delete [options] - yams delete –name [options] - yams delete –names [options] - yams delete –pattern [options]

Options: - –name - Delete a document by its name - –names - Delete multiple documents by names (comma-separated) - –pattern - Delete documents matching a glob pattern (e.g., .log, temp_.txt) - –force, –no-confirm - Skip confirmation prompt - –dry-run - Preview what would be deleted without actually deleting - –keep-refs - Keep reference counts (don’t decrement) - -v, –verbose - Show detailed deletion progress

Description: - Supports deletion by hash (original behavior), name, multiple names, or pattern matching. - When deleting by name and multiple documents have the same name, you’ll be prompted to confirm unless –force is used. - Pattern matching supports standard glob patterns (* for any characters, ? for single character). - Dry-run mode shows what would be deleted without making changes. - Bulk deletions show progress and report both successes and failures.

Examples: 

# Delete by hash (original)
yams delete abcd1234...
yams rm abcd1234...  # Using alias

# Delete by name
yams delete --name "meeting-notes.txt"
yams rm --name "old-file.txt" --force  # Using alias

# Delete multiple files
yams delete --names "old-report.pdf,draft.txt,temp.log"

# Delete by pattern
yams delete --pattern "*.tmp"
yams delete --pattern "backup_*.zip" --dry-run

# Force deletion without confirmation
yams delete --pattern "temp_*" --force

# Verbose output
yams delete --names "file1.txt,file2.txt" --verbose

list {#cmd-list}

ls {#cmd-ls}

List stored documents with rich metadata display. (Alias: ls)

Synopsis: - yams list [options]

Options: - –format - Output format: table | json | csv | minimal (default: table) - -l, –limit - Maximum number of documents to list (default: 100) - –offset - Offset for pagination (default: 0) - –recent - Show N most recent documents - –sort - Sort by: name | size | date | hash (default: date) - -r, –reverse - Reverse sort order - -v, –verbose - Show detailed information - –show-snippets - Show content previews (default: true) - –show-metadata - Show all metadata for each document - –show-tags - Show document tags (default: true) - –snippet-length - Length of content snippets (default: 50) - –no-snippets - Disable content previews

Description: - Displays documents with comprehensive metadata including names, types, sizes, content snippets, tags, and timestamps. - Rich table format shows NAME, TYPE, SIZE, SNIPPET, TAGS, and WHEN columns. - The –recent flag filters to the N most recent documents before applying other sorting options. - Content snippets provide quick previews of document contents. - Multiple output formats support different use cases from human-readable to machine processing.

Examples: 

yams list
yams ls  # Using alias
yams list --recent 10  # Show 10 most recent documents
yams list --sort size --reverse  # Sort by size, largest first
yams list --format json
yams ls --format csv --limit 50  # Using alias
yams list --format minimal --offset 20
yams list --no-snippets --show-metadata  # No previews, full metadata

Tree-Based Query Optimization (v0.7.5+)

The list command uses tree-based path indexing for efficient queries on large repositories. Path patterns with wildcards (*, **) automatically leverage tree structures for O(log n) performance:

Pattern-based queries (tree-optimized): 

# List all documents under docs/ directory (recursive)
yams list --name "docs/**"

# List all markdown files in src/
yams list --name "src/**/*.md"

# List all files in a specific directory (non-recursive)
yams list --name "project/bin/*"

Combining patterns with filters (tree query + filtering): 

# Documents under docs/ with specific tag
yams list --name "docs/**" --tags "api"

# C++ source files under src/ with multiple tags
yams list --name "src/**/*.cpp" --tags "code,reviewed"

# All text files under project/ by MIME type
yams list --name "project/**" --mime "text/plain"

# Files by extension under specific path
yams list --name "examples/**" --extension ".json"

# Combined filters for precise results
yams list --name "src/**" --tags "test" --extension ".cpp" --mime "text/x-c++"

Performance notes: - Tree queries with path prefixes: ~160 μs per query (6.25k queries/sec) - Tree queries with filters: 100-126 μs per query (up to 10k queries/sec) - Filters can improve performance by reducing result set size - Use /** for recursive directory matching, /* for single-level - Patterns are automatically canonicalized on macOS to handle /var → /private/var symlinks

Best practices: - Prefer tree-based patterns (path/**) over substring matches for better performance - Combine multiple filters to narrow results efficiently - Use --format json with tree queries for programmatic processing

Snapshot Operations (Enhanced in PBI-043)

The list command has been enhanced with smart snapshot and file history capabilities:

List all snapshots: 

yams list --snapshots
yams list --snapshots --format json
yams list --snapshots --collection myproject

Show file history across snapshots: 

# Shows timeline of changes (Added, Modified, Renamed) across all snapshots
yams list src/main.cpp

# Output example:
# File: src/main.cpp
# 
# Snapshot History:
# v1.2  2025-10-01 14:30  Modified  hash: abc123...  2.5 KB  (current)
# v1.1  2025-09-22 10:15  Modified  hash: def456...  2.3 KB  
# v1.0  2025-09-15 09:00  Added     hash: ghi789...  2.1 KB

Show file at specific snapshot: 

yams list src/main.cpp --snapshot-id=v1.0

# Output shows metadata and suggests next actions:
# File: src/main.cpp (v1.0)
# Size: 2.1 KB
# Hash: ghi789...
# 
# Use 'yams cat src/main.cpp --snapshot-id=v1.0' to view content
# Use 'yams list src/main.cpp' to see history across all snapshots

Compare file between snapshots (inline diff): 

yams list src/main.cpp --snapshot-id=v1.0 --compare-to=v1.1

# Shows inline diff with syntax highlighting:
# File: src/main.cpp
# Comparing: v1.0 → v1.1
# 
# @@ -10,6 +10,8 @@
#  int main(int argc, char** argv) {
# +    // Initialize logging
# +    initLogger();
#      processArgs(argc, argv);
#      return runApp();
#  }

Smart behavior: - yams list → List all documents - yams list --snapshots → List all available snapshots - yams list <filepath> → Show file history across snapshots - yams list <filepath> --snapshot-id=X → Show file at snapshot X - yams list <filepath> --snapshot-id=X --compare-to=Y → Inline diff

The command automatically detects file paths (contain / or .) and adapts its behavior accordingly.

diff {#cmd-diff}

Compare two snapshots and show file changes with tree diff.

New in PBI-043: Efficient snapshot comparison using Merkle tree diffs with rename detection.

Synopsis: - yams diff [options]

Options: - –format - Output format: tree (default) | flat | json - tree: Structured diff with rename detection (recommended) - flat: Legacy flat diff without rename tracking - json: Machine-readable output for tools - –include - Include only files matching patterns (comma-separated globs) - Example: –include=”.cpp,.h” - –exclude - Exclude files matching patterns (comma-separated globs) - Example: –exclude=”.log,.tmp,build/**” - –type - Filter by change type: added | deleted | modified | renamed - Example: –type=modified (show only modified files) - –stats - Show only summary statistics (no file list) - –no-renames - Disable rename detection (faster, but less accurate) - -v, –verbose - Show detailed information including file hashes

Description: - Compares two snapshots and displays changes using efficient tree diff algorithm. - Rename detection: Automatically detects moved/renamed files by matching content hashes. - O(log n) subtree matching: Unchanged subtrees are skipped for performance. - Changes are grouped by type: Added, Deleted, Modified, Renamed, Moved. - Tree format is the default and recommended for most use cases.

Examples: 

# Basic diff
yams diff v1.0 v1.1

# Output example:
# Comparing v1.0 → v1.1
# 
# Added (6 files):
#   + src/new-feature.cpp
#   + src/new-feature.h
#   + tests/test_new_feature.cpp
#   + docs/new-feature.md
#   + lib/dependency.so
#   + config/feature-flags.json
# 
# Deleted (2 files):
#   - src/deprecated.cpp
#   - src/deprecated.h
# 
# Modified (3 files):
#   ~ src/main.cpp                 (2.3 KB → 2.5 KB)
#   ~ README.md                     (1.1 KB → 1.3 KB)
#   ~ Makefile                      (845 B → 920 B)
# 
# Renamed (1 file):
#   → src/utils.cpp → src/common/utils.cpp
# 
# Summary:
#   +6 files added
#   -2 files deleted
#   ~3 files modified
#   →1 file renamed
#   Total: 12 changes

# Filter by file type
yams diff v1.0 v1.1 --include="*.cpp,*.h"

# Show only modified files
yams diff v1.0 v1.1 --type=modified

# Show summary statistics only
yams diff v1.0 v1.1 --stats

# Output example (stats):
# Snapshot Comparison: v1.0 → v1.1
#   Files added:    6
#   Files deleted:  2
#   Files modified: 3
#   Files renamed:  1
#   Total changes:  12

# JSON output for tools
yams diff v1.0 v1.1 --format=json

# Legacy flat diff (convenience flag)
yams diff v1.0 v1.1 --flat-diff
# Or equivalently:
yams diff v1.0 v1.1 --format=flat

# Compare specific directory
yams diff v1.0 v1.1 --include="src/**"

# Exclude build artifacts
yams diff v1.0 v1.1 --exclude="build/**,*.o,*.so"

# Verbose output with hashes
yams diff v1.0 v1.1 -v

Performance Notes: - Tree diff is computed in O(log n) time when trees are pre-built during yams add. - If trees don’t exist, they will be computed on-demand (may be slower for large snapshots). - Use --no-renames to skip rename detection for faster results on very large diffs.

See Also: - yams list --snapshots - List available snapshots - yams list <file> - Show file history across snapshots - yams add --snapshot-id - Create snapshots

Note: Default search type is hybrid. When strict/hybrid returns zero results, the CLI auto-retries with fuzzy (similarity 0.7).

YAMS-first code search Always use YAMS to search the indexed codebase (no external grep/find/rg).

Examples: 

# List only file paths for efficient context
yams search "IndexingPipeline" --paths-only

# Fuzzy search for broader discovery
yams search "vector database" --fuzzy --similarity 0.7 --paths-only

# Restrict by extension via keyword filters
yams search "class DocumentIndexer ext:.cpp" --paths-only

# Show JSON for scripting
yams search "SyncManager" --json

# Queries that start with '-' (option-looking) — pass safely
yams search -q "--start-group --whole-archive --end-group -force_load Darwin" --paths-only
yams search -- "--start-group --whole-archive --end-group -force_load Darwin" --paths-only
printf '%s\n' "--start-group --whole-archive --end-group -force_load Darwin" | yams search --stdin --paths-only
yams search --query-file /tmp/query.txt --paths-only
yams search --query-file - --paths-only < /tmp/query.txt

Hints: - Prefer hybrid or fuzzy search for exploratory queries; narrow with exact keywords as you iterate. - Combine with –paths-only to feed subsequent yams get calls. - Session helpers (experimental): Use yams session pin|list|unpin|warm to manage hot data. See PROMPT docs for examples: ../PROMPT-eng.md and ../PROMPT.md

Search for documents with advanced query capabilities.

Synopsis: - yams search “” [options] - yams search -q “” [options] - yams search –stdin [options] - yams search –query-file [options]

Options: - -q, –query - Provide the query as an option (useful when it starts with ‘-‘) - –stdin - Read query from standard input when no query is provided - –query-file - Read query from a file path (use ‘-’ to read from stdin) - -l, –limit - Maximum number of results to return (default: 20) - -t, –type - Search type: keyword | semantic | hybrid (default: hybrid) - -f, –fuzzy - Enable fuzzy search for approximate matching - –similarity - Minimum similarity for fuzzy search, 0.0-1.0 (default: 0.7) - –hash - Search by file hash (full or partial, minimum 8 characters) - -n, –line-numbers - Show line numbers with matches - -A, –after - Show N lines after match (default: 0) - -B, –before - Show N lines before match (default: 0) - -C, –context - Show N lines before and after match (default: 0)

Description: - Supports both exact keyword searches and fuzzy approximate matching. - Fuzzy search uses BK-tree indexing for efficient similarity matching with configurable thresholds. - Full-text search with FTS5 indexing provides fast document content queries with robust special character handling. - Hash search allows finding documents by their SHA256 hash (full 64-character hash or partial prefix). - Automatic fallback: if FTS5 query fails (due to special characters), automatically falls back to fuzzy search. - Robust query sanitization handles special characters like hyphens, quotes, and operators (e.g., “PBI-6”, “task 4-“). - JSON output includes relevance scores, execution times, and content snippets. - Searches document names, content, tags, and metadata fields. - Auto-detects hash format: if query looks like a hash (8-64 hex chars), automatically searches by hash. - Verbosity control: concise output by default, detailed output with –verbose flag.

Examples: 

# Text search
yams search "database performance"
yams search "config file" --fuzzy --similarity 0.6
yams search "meeting notes" --limit 10 --type keyword
yams search "project roadmap" --json

# Hash search
yams search --hash abcd1234ef567890  # Partial hash (minimum 8 chars)
yams search --hash abcd1234ef567890abcd1234ef567890abcd1234ef567890abcd1234ef567890  # Full hash
yams search abcd1234ef567890  # Auto-detected hash search

# Verbose output for detailed information
yams search "query" --verbose
yams search --hash abcd1234 --verbose

grep {#cmd-grep}

Regex across indexed code (YAMS only, hybrid by default) Use YAMS grep for project-wide regex; avoid system utilities for repository queries.

Examples: 

# Find class definitions
yams grep "class\\s+IndexingPipeline" --include="**/*.hpp,**/*.cpp"

# Locate TODOs in headers and sources
yams grep "TODO\\b" --include="**/*.hpp,**/*.h,**/*.cpp"

# Search for CLI subcommand declarations
yams grep "##\\s+(watch|git|sync)\\b" --include="**/*.md"

Notes: - Default mode is hybrid: regex plus semantic suggestions; use –regex-only to disable. Tune with –semantic-limit (default: 10). - Semantic suggestions are also shown in -l/–files-with-matches, -L/–files-without-match, –paths-only, and -c/–count modes. Regex counts only reflect text matches. - Hot/Cold modes: control behavior via environment variables. For grep, set YAMS_GREP_MODE=hot_only|cold_only|auto (hot uses extracted text cache; cold scans CAS bytes). For list, use YAMS_LIST_MODE, and for retrieval (cat/get), use YAMS_RETRIEVAL_MODE. - –include accepts comma-separated globs or repeated usage; prefer quoting patterns. - Pair with yams search –paths-only to scope subsequent grep runs.

Search for regex patterns within file contents.

Synopsis: - yams grep [paths…] [options]

Options: - -A, –after - Show N lines after match (default: 0) - -B, –before - Show N lines before match (default: 0) - -C, –context - Show N lines before and after match (default: 0) - -i, –ignore-case - Case-insensitive search - -w, –word - Match whole words only - -v, –invert - Invert match (show non-matching lines) - -n, –line-numbers - Show line numbers - -H, –with-filename - Show filename with matches - –no-filename - Never show filename - -c, –count - Show only count of matching lines - -l, –files-with-matches - Show only filenames with matches - -L, –files-without-match - Show only filenames without matches - –color - Color mode: always, never, auto (default: auto) - –max-count - Stop after N matches per file - –limit - Alias for –max-count

Description: - Searches through the content of all indexed files using regular expressions. - Supports standard grep-like options for context, case sensitivity, and output control. - Automatically highlights matches when outputting to a terminal. - Can search all indexed files or specific paths. - Uses ECMAScript regex syntax for pattern matching.

Examples: 

# Basic pattern search
yams grep "TODO"
yams grep "error.*failed" -i

# With context
yams grep "function" -C 2
yams grep "class.*Repository" -A 5

# File listing
yams grep "deprecated" -l
yams grep "test" src/ -c

# Complex patterns
yams grep "^import.*from" -n
yams grep "\bclass\s+\w+Command\b" --color=always

config {#cmd-config}

Manage YAMS configuration settings.

Subcommands: - get - Print a configuration value. - set - Update a configuration value. - list - Print all keys/values. - validate [–config-path ] - Validate configuration. - export [–format toml|json] - Output current configuration. - embeddings - Manage embedding configuration (model, dimensions). - search - Manage search configuration. - grammar - Manage tree-sitter grammars for symbol extraction. - tuning - Manage daemon tuning settings. - storage - Configure storage settings. - migrate - Migrate configuration to v2. - update - Add newly introduced v2 keys without overwriting existing values. - check - Check if config needs migration.

Examples: 

yams config list
yams config get core.data_dir
yams config set embeddings.preferred_model all-MiniLM-L6-v2
yams config validate
yams config export --format json
yams config grammar list              # List available grammars
yams config grammar download cpp      # Download C++ grammar

auth {#cmd-auth}

Manage authentication material (keys, tokens, API keys). Availability and exact options depend on your build.

Examples: 

yams auth --help

stats {#cmd-stats}

Show storage statistics and health.

Synopsis: - yams stats [options]

Description: - Adaptive default view: when relevant, includes Recommendations and Service Status along with the compact footer; use -v for full System Health and detailed sections. - Telemetry includes auto-repair counters (repair_queue_depth, repair_batches_attempted, repair_embeddings_generated, repair_failed_operations), latency percentiles (p50/p95), top_slowest components, and not_ready flags. - Use –json for machine-readable output.

Examples: 

yams stats
yams stats -v
yams stats --json

uninstall {#cmd-uninstall}

Remove YAMS data/config from the system.

Synopsis: - yams uninstall [–force]

Warning: - This is destructive. Make sure you have backups.

Examples: 

yams uninstall
yams uninstall --force

migrate {#cmd-migrate}

Run metadata migrations if any are pending.

Synopsis: - yams migrate

Examples: 

yams migrate

update {#cmd-update}

Update metadata for existing documents.

Synopsis: - yams update –metadata … - yams update –name –metadata …

Options: - hash - Document hash (full or partial) to update - –name - Document name to update (useful for stdin documents) - -m, –metadata - Metadata key-value pairs to set (can be specified multiple times) - -v, –verbose - Show detailed update information

Notes: - Either hash or –name must be specified, but not both - Multiple metadata pairs can be updated in a single command - Existing metadata values will be overwritten - Works with both file-based and stdin documents - If multiple documents have the same name, you’ll be prompted to use the hash

Examples: 

# Update by hash
yams update fc8fc5fa --metadata "status=completed" --metadata "reviewed=true"

# Update by name  
yams update --name "project-notes.md" --metadata "priority=high"

# Update stdin document
yams update --name "arxiv-2402.05391" --metadata "read=true" --metadata "rating=5"

# Task tracking example
yams update --name "task-001.md" --metadata "status=in_progress" --metadata "assignee=alice"

model {#cmd-model}

Manage embedding models: list installed, download new, inspect, and verify runtime.

Synopsis: - yams model list - yams model download [–url ] - yams model info - yams model check

Description: - list: Shows locally available models (autodiscovers ~/.yams/models//model.onnx and other configured roots) - download: Fetches a model by name; use –url to override with a custom ONNX URL - info: Prints details for a model (dimensionality, path, notes when available) - check: Verifies ONNX runtime support, plugin directory status, and autodiscovery paths

Configuring the preferred model: - yams config embeddings model # sets embeddings.preferred_model - embeddings.model_path can point to the models root; name-based resolution order: configured root → ~/.yams/models → models/ → /usr/local/share/yams/models

Examples: 

yams model list
yams model download all-MiniLM-L6-v2
yams model download my-custom --url https://example.com/models/custom.onnx
yams model info all-MiniLM-L6-v2
yams model check
yams config embeddings model all-MiniLM-L6-v2

plugin {#cmd-plugin}

Manage plugins: scanning, trust policy, load/unload, install, and info.

Synopsis: - yams plugin list - yams plugin scan [–dir DIR] [TARGET] - yams plugin info - yams plugin health - yams plugin load - yams plugin unload - yams plugin trust add | list | remove - yams plugin install - yams plugin uninstall - yams plugin update [name] - yams plugin repo [query] - yams plugin search

Subcommands: - list: Show loaded plugins and their interfaces. - scan: Inspect directories for plugins without initializing; prints name/version/ABI. - info: Show manifest/health JSON for a loaded plugin. - health: Show health status of loaded plugins. - load: Load a plugin by absolute path or name; respects trust policy. - unload: Unload a plugin by name. - trust: Manage the trust policy file ~/.config/yams/plugins_trust.txt. - install: Install plugin from repository or URL. - uninstall: Uninstall a plugin. - update: Update plugins to latest version. - repo: Query plugin repository. - search: Search plugin catalog (local index.json). - enable/disable: Enable/disable plugins (stub). - verify: Verify plugin signature/hash (stub).

Notes: - Default discovery order: YAMS_PLUGIN_DIR (exclusive if set), $HOME/.local/lib/yams/plugins, /usr/local/lib/yams/plugins, /usr/lib/yams/plugins, and ${CMAKE_INSTALL_PREFIX}/lib/yams/plugins. - The daemon prefers host-backed model_provider_v1 when an ONNX plugin is trusted/loaded; otherwise it falls back to the legacy registry or mock/null provider. - Disable plugin subsystem: start the daemon with --no-plugins.

Examples: 

# Discover and trust a system plugins directory
yams plugin scan
yams plugin trust add /usr/local/lib/yams/plugins
yams plugin trust list

# Load ONNX plugin by path (respects trust policy)
yams plugin load /usr/local/lib/yams/plugins/libyams_onnx_plugin.so

# Check plugin health
yams plugin health

# Inspect and unload
yams plugin info onnx
yams plugin unload onnx

doctor {#cmd-doctor}

Diagnose daemon connectivity, model/provider readiness, vector DB dimensions, and plugins. Includes repair helpers.

Synopsis: - yams doctor [OPTIONS] - yams doctor daemon - yams doctor plugin [] - yams doctor plugins - yams doctor embeddings - yams doctor repair [–embeddings] [–fts5] [–graph] [–all] - yams doctor validate - yams doctor dedupe - yams doctor prune - yams doctor tuning

Subcommands: - daemon: Check daemon socket and status - plugin: Check a specific plugin (.so/.wasm or by name) - plugins: Show plugin summary (loaded + scan) - embeddings: Embeddings diagnostics and actions - repair: Repair common issues (embeddings, FTS5, graph) - validate: Validate knowledge graph health - dedupe: Detect (and optionally remove) duplicate documents - prune: Remove build artifacts, logs, cache, and temporary files - tuning: Auto-configure [tuning] based on system baseline

Options: - –json: Output results in JSON format - –fix: Fix everything (embeddings + FTS5) - –fix-config-dims: Align config embedding dims to target (non-interactive) - –recreate-vectors: Drop and recreate vector tables to target dim - –dim : Target dimension to use with –recreate-vectors - –stop-daemon: Attempt to stop daemon before DB operations

Highlights: - Summary shows daemon status, vector DB dimension vs model target, and loaded plugins. - Knowledge Graph section appears when available; if empty, recommends: yams doctor repair --graph to build from tags/metadata.

Repair options: - –embeddings: Generate missing document embeddings (daemon streaming when available; local fallback). - –fts5: Rebuild the text index best-effort. - –graph: Construct/repair the knowledge graph from tags/metadata. - –all: Run all repair operations.

Examples: 

yams doctor
yams doctor --json
yams doctor plugin onnx
yams doctor plugins
yams doctor repair --graph
yams doctor repair --all
yams doctor --recreate-vectors --dim 768 --stop-daemon
yams doctor dedupe --dry-run
yams doctor prune
yams doctor tuning

repair {#cmd-repair}

Run storage/database maintenance and (optionally) embedding generation.

Synopsis: - yams repair [OPTIONS]

Options: - –orphans: Clean orphaned metadata entries - –chunks: Remove orphaned chunk files and reclaim space - –mime: Fix missing MIME types in documents - –fts5: Rebuild FTS5 index for documents (best-effort) - –embeddings: Generate missing vector embeddings - –checksums: Verify and repair checksums - –duplicates: Find and optionally merge duplicates - –downloads: Repair download documents (add tags/metadata, normalize names) - –path-tree: Rebuild path tree index for documents missing from the tree - –optimize: Vacuum/optimize the database - –all: Run all repair operations - –dry-run: Preview operations without making changes - –force: Skip confirmations - –foreground: Run embeddings repair in foreground (stream progress) - –include-mime : Additional MIME types to embed (e.g., application/pdf), repeatable - –model : Embedding model to use (overrides preferred) - –stop-daemon: Attempt to stop daemon before vector DB operations - -v, –verbose: Show detailed progress

Notes: - By default, embedding repair targets text-like MIME types only; binaries (PDFs/images) are skipped unless explicitly included with –include-mime. - PDF text extraction and embedding depend on build configuration (PDF support must be available).

Examples: 

yams repair --all --dry-run
yams repair --orphans --chunks --optimize --force
yams repair --embeddings
yams repair --embeddings --include-mime application/pdf
yams repair --fts5 --verbose
yams repair --path-tree

status {#cmd-status}

Show service readiness, subsystem health, and runtime stats (daemon-aware).

Synopsis: - yams status

Description: - Prints a concise services summary (e.g., ✓ Content | ✓ Repo | ✓ Search | ⚠ (N) Models) - During initialization, shows a WAIT line with not-ready components and progress - Exposes fields such as running/ready state, uptime, request counts, active connections, memory, CPU, and version when available - Highlights top slowest components and actionable recommendations when relevant

Tips: - Use yams stats -v for detailed system health, recommendations, and service status sections. - Bootstrap status file: ~/.local/state/yams/yams-daemon.status.json

Examples: 

yams status

daemon {#cmd-daemon}

Control the background daemon (if included in your build).

Synopsis: - yams daemon start - yams daemon stop - yams daemon status - yams daemon restart

Description: - start/stop/restart the daemon process - status shows readiness and subsystem overview similar to yams status

Notes: - When client/daemon protocol versions differ, a one-time warning may be shown; upgrade the daemon if features appear limited.

Examples: 

yams daemon status
yams daemon restart

serve {#cmd-serve}

Start the MCP (Model Context Protocol) server over stdio.

Synopsis: - yams serve [OPTIONS]

Options: - –daemon-socket - Override daemon socket path (env: YAMS_DAEMON_SOCKET) - –verbose - Show startup banner and enable info-level logging (default: quiet mode)

Description: - Exposes YAMS functionality through the Model Context Protocol for AI tool integration. - Uses stdio transport (JSON-RPC over stdin/stdout) for direct AI integration. - Provides search, retrieval, and document management capabilities to AI systems. - Graceful shutdown on SIGINT/SIGTERM signals. - Server runs quietly by default; use –verbose for startup banner.

Examples: 

# Start MCP server (default quiet mode)
yams serve

# With verbose logging
yams serve --verbose

# With custom daemon socket
yams serve --daemon-socket /tmp/yams.sock

completion {#cmd-completion}

Generate shell completion scripts for popular shells.

Synopsis: - yams completion bash - yams completion zsh - yams completion fish - yams completion powershell

Notes: - Bash: if bash-completion isn’t installed, a minimal fallback is baked into the script. - Zsh: the generated script auto-runs compinit if needed to prevent “_arguments: command not found”. - Fish: installs via standard fish completions. - PowerShell: uses Register-ArgumentCompleter for native tab completion.

Installation Instructions

Bash (Linux/macOS): 

# Quick use without installing
source <(yams completion bash)

# Install for current user
mkdir -p ~/.local/share/bash-completion/completions
yams completion bash > ~/.local/share/bash-completion/completions/yams

# Or install system-wide (requires sudo)
yams completion bash | sudo tee /etc/bash_completion.d/yams > /dev/null

Zsh (Linux/macOS): 

# Quick use without installing
source <(yams completion zsh)

# Install for current user (Oh My Zsh)
yams completion zsh > ~/.oh-my-zsh/completions/_yams

# Or standard location
mkdir -p ~/.local/share/zsh/site-functions
yams completion zsh > ~/.local/share/zsh/site-functions/_yams

Fish: 

yams completion fish > ~/.config/fish/completions/yams.fish

PowerShell (Windows/Linux/macOS): 

# Quick use for current session
Invoke-Expression (yams completion powershell | Out-String)

# Install permanently (add to profile)
yams completion powershell | Out-File -Encoding utf8 $PROFILE.CurrentUserAllHosts -Append

# Or create a separate completion file
$completionPath = "$HOME\.config\yams\completions"
New-Item -ItemType Directory -Path $completionPath -Force
yams completion powershell | Out-File -Encoding utf8 "$completionPath\yams.ps1"
# Then add to your profile: . "$HOME\.config\yams\completions\yams.ps1"

Verifying Installation

After installing, restart your shell or reload your profile:

# Bash/Zsh
source ~/.bashrc   # or ~/.zshrc

# PowerShell
. $PROFILE

Then test by typing yams and pressing Tab.

Exit Codes

  • 0 Success.
  • 1 General error (unexpected exception or failure).
  • Non-zero values may indicate specific errors depending on the subcommand.

Snapshot Workflows

New in PBI-043: Efficient snapshot management with Merkle tree diffs and rename detection.

Overview

Snapshots provide point-in-time captures of your repository content. YAMS automatically builds Merkle trees during yams add --snapshot-id operations, enabling fast O(log n) diff comparisons between snapshots.

Basic Workflow

1. Initial import (automatic snapshot): 

# Capture current state of source code
yams add . --recursive \
  --include="*.cpp,*.hpp,*.h,*.md" \
  --label "Initial release" \
  --tags "code,release"

# Snapshot created automatically: 2025-10-01T09:00:00.000Z

2. Make changes to your codebase: 

# Edit files, add features, fix bugs...
vim src/main.cpp
git commit -am "Added new feature"

3. Capture updated state (automatic snapshot): 

# Just add again - snapshot created automatically
yams add . --recursive \
  --include="*.cpp,*.hpp,*.h,*.md" \
  --label "Feature release" \
  --tags "code,release"

# New snapshot: 2025-10-01T14:30:00.000Z

4. Compare snapshots: 

# List snapshots to find timestamp IDs
yams list --snapshots

# Compare using timestamp IDs (fast O(log n) tree diff)
yams diff 2025-10-01T09:00:00.000Z 2025-10-01T14:30:00.000Z

# Output example:
# Comparing v1.0 → v1.1
# 
# Added (3 files):
#   + src/new-feature.cpp
#   + src/new-feature.h
#   + tests/test_new_feature.cpp
# 
# Modified (2 files):
#   ~ src/main.cpp                 (2.3 KB → 2.5 KB)
#   ~ README.md                     (1.1 KB → 1.3 KB)
# 
# Renamed (1 file):
#   → src/utils.cpp → src/common/utils.cpp
# 
# Summary: 6 changes (+3, ~2, →1)

Snapshot Discovery

List all snapshots: 

yams list --snapshots

# Output example (chronological, newest first):
# Snapshot ID                  Label              Collection      Files  Date
# 2025-10-01T14:30:00.000Z    Feature release    -               125    2025-10-01 14:30
# 2025-09-20T10:15:00.000Z    Updated docs       documentation    45    2025-09-20 10:15
# 2025-09-15T09:00:00.000Z    Initial release    -               122    2025-09-15 09:00

Filter by collection: 

yams list --snapshots --collection=releases

JSON output for tools: 

yams list --snapshots --format=json | jq '.[] | select(.label | contains("release"))'

File History Tracking

View file history across snapshots: 

yams list src/main.cpp

# Output example:
# File: src/main.cpp
# 
# Snapshot History:
# v1.1  2025-10-01 14:30  Modified  hash: abc123...  2.5 KB  (current)
# v1.0  2025-09-15 09:00  Added     hash: def456...  2.3 KB

View file at specific snapshot: 

# See metadata
yams list src/main.cpp --snapshot-id=v1.0

# View content
yams cat src/main.cpp --snapshot-id=v1.0

# Restore to disk
yams get --name src/main.cpp --snapshot-id=v1.0 -o main-v1.0.cpp

Inline diff between snapshots: 

yams list src/main.cpp --snapshot-id=v1.0 --compare-to=v1.1

# Shows inline diff with syntax highlighting

Advanced Diff Operations

Filter by file type: 

# Show only C++ changes
yams diff v1.0 v1.1 --include="*.cpp,*.hpp"

# Exclude build artifacts
yams diff v1.0 v1.1 --exclude="build/**,*.o"

Filter by change type: 

# Show only added files
yams diff v1.0 v1.1 --type=added

# Show only renames (useful for tracking file moves)
yams diff v1.0 v1.1 --type=renamed

Summary statistics: 

yams diff v1.0 v1.1 --stats

# Output:
# Snapshot Comparison: v1.0 → v1.1
#   Files added:    3
#   Files deleted:  0
#   Files modified: 2
#   Files renamed:  1
#   Total changes:  6

JSON output for tools: 

yams diff v1.0 v1.1 --format=json > diff.json

# Analyze with jq:
jq '.changes[] | select(.type == "modified")' diff.json

Verbose output with hashes: 

yams diff v1.0 v1.1 -v

# Shows full file hashes for each change

Collections and Organization

Organize snapshots by collection: 

# Development snapshots
yams add src/ --recursive --collection=dev --snapshot-id=dev-2025-10-01

# Documentation snapshots
yams add docs/ --recursive --collection=documentation --snapshot-id=docs-v3

# Release snapshots
yams add . --recursive --collection=releases --snapshot-id=v2.0 --snapshot-label="Major release"

Compare within collections: 

yams list --snapshots --collection=releases
yams diff v1.0 v2.0  # Compare releases

Restoration Workflows

Restore entire snapshot: 

# Restore to specific directory
yams restore --snapshot-id=v1.0 --output-directory=./restore-v1.0

# Preview without writing files
yams restore --snapshot-id=v1.0 --output-directory=./test --dry-run

# Overwrite existing files
yams restore --snapshot-id=v1.0 --output-directory=. --overwrite

Selective restoration: 

# Restore only specific file types
yams restore --snapshot-id=v1.0 \
  --output-directory=./restore \
  --include-patterns="*.cpp,*.h"

# Exclude directories
yams restore --snapshot-id=v1.0 \
  --output-directory=./restore \
  --exclude-patterns="build/**,third_party/**"

Restore by collection: 

yams restore-collection --collection=releases --output-directory=./releases

Performance Characteristics

Tree-based diff performance: - Small changes (< 1%): O(log n) subtree matching, ~100x faster than flat diff - Large changes (> 50%): Approaches O(n) but still faster due to hash-based comparison - Rename detection: Hash-based matching is O(n) but only runs on Added/Deleted pairs

Storage efficiency: - Merkle trees are stored once in CAS and deduplicated across snapshots - Unchanged subtrees share the same tree hash (deduplication) - Tree overhead: ~5-10% additional storage for large repositories - Diff computation: ~5-10% slower during yams add --snapshot-id (tree building)

Optimization tips: - Use --exclude patterns to skip build artifacts, caches, and temporary files - Use --no-renames for faster diff when rename tracking isn’t needed - Pre-build trees during snapshot creation for instant diff operations

Integration with Git

Automatic git integration: When yams add runs in a git repository, snapshot metadata automatically includes: - git_commit: Current commit hash (e.g., abc123def456) - git_branch: Current branch name (e.g., main, develop) - git_remote: Remote repository URL (if configured)

This creates a natural bidirectional link between YAMS snapshots and git history.

Snapshot on git commit (hook): 

#!/bin/bash
# Hook: .git/hooks/post-commit
# Automatically snapshot on every commit
yams add . --recursive \
  --include="*.cpp,*.hpp,*.h,*.md" \
  --label "$(git log -1 --pretty=%B | head -1)" \
  --tags "code,git,auto"

Snapshot on git tag: 

#!/bin/bash
# Hook: .git/hooks/post-tag
TAG=$(git describe --tags --abbrev=0)
yams add . --recursive \
  --include="*.cpp,*.hpp,*.h,*.md" \
  --label="Git tag: $TAG" \
  --tags "code,git,release"

Daily snapshots: 

#!/bin/bash
# Cron: daily snapshot at midnight
yams add . --recursive \
  --include="*.cpp,*.hpp,*.h,*.md" \
  --label="Daily backup" \
  --tags "code,daily"
# Snapshot ID is auto-generated with current timestamp

Troubleshooting

Missing trees: 

# If diff is slow, trees may not exist
# Rebuild trees for existing snapshots:
yams list --snapshots  # Find snapshot IDs
yams doctor repair --snapshots  # Rebuild missing trees (future feature)

Large diff output: 

# Use filters to reduce output
yams diff v1.0 v2.0 --type=modified --include="src/**"
yams diff v1.0 v2.0 --stats  # Summary only

Restore conflicts: 

# Preview first
yams restore --snapshot-id=v1.0 --output-directory=./test --dry-run

# Use overwrite cautiously
yams restore --snapshot-id=v1.0 --output-directory=. --overwrite

Best Practices

  1. Use labels liberally: Labels make snapshot timelines human-readable (--label "Before refactor")
  2. Leverage automatic IDs: No need to manually manage snapshot IDs - timestamps provide natural ordering
  3. Exclude build artifacts: Use --exclude="build/**,*.o,*.so" to reduce noise and improve performance
  4. Tag meaningful snapshots: Use --tags for filtering (e.g., release, milestone, backup)
  5. Collections for organization: Group related content (--collection=releases, --collection=docs)
  6. Automate with git hooks: Snapshot on every commit or tag for complete history tracking
  7. Test restores: Verify snapshots with --dry-run before overwriting files
  8. Trust the timestamps: Snapshot IDs are ISO 8601 timestamps - sort naturally and are globally unique

Tips

YAMS-first workflow (until watch/track is available) - Always search the codebase with YAMS (search/grep). Do not use system grep/find/rg for repository queries. - After editing code, re-index affected files or directories via yams add (pre-watch workflow). - Use –paths-only for path lists you can pipe into further commands or editors. - Prefer –include with comma-separated patterns (e.g., “.cpp,.hpp,*.h”) to bound searches and indexing. - Retrieve exact files for review with yams get –name -o . - Keep tags consistent (e.g., code,source; code,headers; code,working) and update metadata with yams update as needed.

  • Use –json where supported to integrate with scripts and tools.
  • Specify a storage directory explicitly with –storage or via YAMS_STORAGE to keep data separate for testing vs production.
  • When available, use –help –verbose for detailed per-command help, or yams –help-all for the full reference in the terminal.