@precisionutilityguild/liquid-shadow 1.0.0

package/LICENSE

@@ -0,0 +1,184 @@
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package/README.md

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+# 🌑 Liquid Shadow
+
+[![Version](https://img.shields.io/badge/version-1.0.0-blue.svg)](https://github.com/PrecisionUtilityGuild/liquid-shadow)
+[![License: Proprietary](https://img.shields.io/badge/License-Proprietary-red.svg)]()
+[![Build Status](https://img.shields.io/badge/build-passing-brightgreen.svg)]()
+
+**Tactical Repository Intelligence Operative - The AI-First Intelligence Layer.**
+
+Liquid Shadow transforms any codebase into a high-signal knowledge graph. It is built **exclusively for AI Agents** to navigate, reason about, and modify large-scale polyglot repositories with precision and token efficiency.
+
+---
+
+## MCP-First Quick Start
+
+Liquid Shadow is primarily an **MCP (Model Context Protocol) Server**. It is the bridge between your reasoning engine and the raw filesystem.
+
+### 1. Consumption Model
+
+Since Liquid Shadow is a tactical tool, we recommend consuming it via **npx** to ensure you always have the latest intelligence layer:
+
+```bash
+# General use (CLI)
+npx @precisionutilityguild/liquid-shadow [command]
+```
+
+### 2. Connect to your Agent
+
+Add the following to your MCP configuration (e.g., `claude_desktop_config.json`):
+
+```json
+{
+  "mcpServers": {
+    "liquid-shadow": {
+      "command": "npx",
+      "args": ["-y", "@precisionutilityguild/liquid-shadow", "liquid-shadow-mcp"]
+    }
+  }
+}
+```
+
+### 3. Tactical Onboarding (The Mission Loop)
+
+Once connected, your agent should follow the **Intelligence Lifecycle**:
+
+```typescript
+// 🛡️ RECON: Initialize the intelligence index
+shadow_recon_onboard({ repoPath: '.' });
+shadow_sync_trace({ repoPath: '.' });
+
+// 📦 SESSION CONTEXT (one call): hologram + chronicle(5) + briefing
+shadow_ops_context({ repoPath: '.' });
+
+// PLAN: Establish the tactical mission
+shadow_ops_plan({
+  repoPath: '.',
+  name: 'Auth Refactor',
+  goal: 'Migrate JWT logic to Session-based auth',
+});
+
+// ANALYZE: Trace the execution flow
+shadow_analyze_flow({
+  repoPath: '.',
+  filePath: 'src/auth/handler.ts',
+});
+
+// LOG: Save architectural decisions (SIGINT)
+shadow_ops_log({
+  missionId: 1,
+  repoPath: '.',
+  type: 'decision',
+  content: 'Selected Redis for session storage due to latency requirements',
+});
+```
+
+---
+
+## Core Tactical Suite
+
+Liquid Shadow is powered by **31 Atomic Tools**, organized into specialized intelligence suites:
+
+| Suite            | Atomic Tools (MCP)                                                                                             | Tactical Purpose                                                                                                 |
+| :--------------- | :------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------- |
+| **Ops Control**  | `shadow_ops_plan`, `_track`, `_briefing`, `_context`, `_log`, `_synthesize`, `_chronicle`, `_health`, `_graph` | Mission management, ADR synthesis; **`_context`** = session start (hologram + chronicle + briefing in one call). |
+| **Intelligence** | `shadow_analyze_impact`, `_flow`, `_deps`, `_debt`                                                             | Deep architectural reasoning and dependency tracing.                                                             |
+| **Discovery**    | `shadow_search_concept`, `_symbol`, `_config`, `_path`                                                         | Semantic and lexical search across the entire graph.                                                             |
+| **Recon**        | `shadow_recon_onboard`, `_tree`, `_hologram`, `_topography`, `_scout`                                          | Structural analysis and layer classification.                                                                    |
+| **Inspection**   | `shadow_inspect_symbol`, `_file`                                                                               | Dense code retrieval with semantic folding.                                                                      |
+| **Maintenance**  | `shadow_sync_trace`, `_index`, `_repair`                                                                       | Intelligence synchronization and Nano-Repair.                                                                    |
+| **Workspace**    | `shadow_workspace_list`, `_link`, `_fuse`                                                                      | Multi-repository mission linking and index fusion.                                                               |
+| **Environment**  | `shadow_env_hooks`, `_diagnose`                                                                                | Git hook automation and system health diagnostics.                                                               |
+
+### 🎯 `shadow_inspect_*` Quick Reference
+
+| I want to...                                       | Mode     | Parameter     | Value                    |
+| -------------------------------------------------- | -------- | ------------- | ------------------------ |
+| See**ALL exports** from a file                     | `file`   | `detailLevel` | `"signatures"` (default) |
+| See**ONE specific symbol** (truncated)             | `symbol` | `context`     | `"definition"` (default) |
+| See**ONE specific symbol** + dependencies + usages | `symbol` | `context`     | `"full"`                 |
+| Just export names (minimal tokens)                 | `file`   | `detailLevel` | `"structure"`            |
+
+---
+
+## Performance
+
+Liquid Shadow is optimized for ultra-fast indexing and semantic retrieval. Performance is benchmarked against enterprise-grade repositories.
+
+### Enterprise Benchmark (Custom Repo)
+
+- **Total Files**: 4,306 files (TS + PHP + PY)
+- **Symbols Extracted**: 22,185 symbols (with deep closure indexing)
+- **Index Time**: 17.8s (Fresh start)
+- **Throughput**: ~242 files/sec
+- **Symbols/sec**: ~1,247 symbols/sec
+- **Note**: Deep closure indexing extracts 30% more symbols (nested functions, closures) compared to top-level-only extraction
+
+### Large-Scale Benchmark (VS Code Core)
+
+- **Total Files**: 6,196 files
+- **Symbols Extracted**: 109,997 symbols (with deep closure indexing)
+- **Index Time**: 116.6s (Fresh start)
+- **Throughput**: ~53 files/sec
+- **Symbols/sec**: ~943 symbols/sec
+- **Scalability**: Verified 100k+ symbol graph support
+
+### High-Volume Benchmark (Next.js)
+
+- **Total Files**: 9,785 files
+- **Symbols Extracted**: 20,701 symbols (with deep closure indexing)
+- **Index Time**: 24.2s (Fresh start)
+- **Throughput**: ~404 files/sec
+- **Symbols/sec**: ~855 symbols/sec
+
+### Running Benchmarks
+
+To benchmark performance on your own repository:
+
+```bash
+npx @precisionutilityguild/liquid-shadow benchmark -- /path/to/repo
+```
+
+---
+
+## Configuration
+
+### Indexing Concurrency
+
+Liquid Shadow allows you to tune indexing concurrency based on your system resources. Higher concurrency speeds up indexing but increases memory usage.
+
+**Environment Variable** (Global):
+
+```bash
+export INDEX_CONCURRENCY=10  # Default: 5
+```
+
+**Repository Config** (Per-Repo):
+Add to `.liquid-shadow.yaml`:
+
+```yaml
+concurrency: 10 # Overrides INDEX_CONCURRENCY for this repo
+```
+
+**Recommendations**:
+
+- **Low-memory systems**: 3-5 (default)
+- **Standard systems**: 5-10
+- **High-memory systems**: 10-20
+- **Very large repos**: Monitor memory usage and adjust accordingly
+
+The concurrency setting controls how many files are processed in parallel during indexing. File parsing is I/O bound, so higher concurrency is beneficial on systems with sufficient RAM.
+
+---
+
+## Documentation
+
+Explore the deeper tactical layers of Liquid Shadow:
+
+- [**Shadow Quick Reference**](./docs/SHADOW_QUICK_REFERENCE.md): **Start here.** Decision flow (“I want to… → use this”), one-liner per tool, and workflow recipes (new chat, understand file, refactor safely, run a mission, multi-repo).
+- [**Skills**](./skills/): Workflow-specific guidance — `understand`, `onboard`, `mission`, `continue`, `chronicle`, `workspace`, `audit`.
+- [**Examples**](./examples/): `mission-tracking`, `onboarding-workflow`, `refactoring-analysis` — concrete flows with Shadow tools.
+
+---
+
+## Key Differentiators
+
+- **Liquid Anchor**: Intelligence that survives refactors and file moves via `shadow_sync_repair`.
+- **Semantic Sieve**: High-signal, token-efficient summaries designed to maximize your context window.
+- **Polyglot Unity**: Unified symbol graph across TypeScript, PHP, Python, Go, and more.
+- **Situational Awareness**: Persistent state via missions and intent logs, allowing for seamless context transitions.
+- **Session-Start Bundle**: `shadow_ops_context` returns hologram + chronicle (last 5) + briefing in one call—ideal for "new chat, give me the world."
+
+---
+
+_Powered by SQLite FTS5, SWC, and Precision Intelligence._
+_Crafted by Precision Utility Guild._

package/dist/data/migrations/001_initial_schema.sql

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+-- Initial database schema with core tables and indexes
+
+CREATE TABLE IF NOT EXISTS files (
+    path TEXT PRIMARY KEY,
+    mtime REAL,
+    last_scanned_at REAL,
+    classification TEXT,
+    summary TEXT,
+    embedding TEXT,
+    content_hash TEXT
+);
+
+CREATE TABLE IF NOT EXISTS exports (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    file_path TEXT,
+    name TEXT,
+    kind TEXT,
+    signature TEXT,
+    doc TEXT,
+    start_line INTEGER,
+    end_line INTEGER,
+    classification TEXT,
+    capabilities TEXT,
+    parent_id INTEGER,
+    embedding TEXT,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE,
+    FOREIGN KEY(parent_id) REFERENCES exports(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS imports (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    file_path TEXT,
+    module_specifier TEXT,
+    imported_symbols TEXT,
+    resolved_path TEXT,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS configs (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    file_path TEXT,
+    key TEXT,
+    value TEXT,
+    kind TEXT,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS file_content (
+    file_path TEXT PRIMARY KEY,
+    content TEXT,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE
+);
+
+-- Indexes
+CREATE INDEX IF NOT EXISTS idx_exports_file_path ON exports(file_path);
+CREATE INDEX IF NOT EXISTS idx_exports_name ON exports(name);
+CREATE INDEX IF NOT EXISTS idx_exports_parent_id ON exports(parent_id);
+CREATE INDEX IF NOT EXISTS idx_exports_classification ON exports(classification);
+CREATE INDEX IF NOT EXISTS idx_imports_file_path ON imports(file_path);
+CREATE INDEX IF NOT EXISTS idx_imports_resolved_path ON imports(resolved_path);
+CREATE INDEX IF NOT EXISTS idx_configs_file_path ON configs(file_path);
+CREATE INDEX IF NOT EXISTS idx_configs_kind ON configs(kind);
+CREATE INDEX IF NOT EXISTS idx_files_classification ON files(classification);
+
+-- DOWN
+DROP INDEX IF EXISTS idx_files_classification;
+DROP INDEX IF EXISTS idx_configs_kind;
+DROP INDEX IF EXISTS idx_configs_file_path;
+DROP INDEX IF EXISTS idx_imports_resolved_path;
+DROP INDEX IF EXISTS idx_imports_file_path;
+DROP INDEX IF EXISTS idx_exports_classification;
+DROP INDEX IF EXISTS idx_exports_parent_id;
+DROP INDEX IF EXISTS idx_exports_name;
+DROP INDEX IF EXISTS idx_exports_file_path;
+DROP TABLE IF EXISTS file_content;
+DROP TABLE IF EXISTS configs;
+DROP TABLE IF EXISTS imports;
+DROP TABLE IF EXISTS exports;
+DROP TABLE IF EXISTS files;

package/dist/data/migrations/002_fts_indexes.sql

@@ -0,0 +1,94 @@
+-- Full-text search (FTS5) tables and triggers
+
+-- FTS5 for exports (symbol search)
+CREATE VIRTUAL TABLE IF NOT EXISTS exports_fts USING fts5(
+    name,
+    signature,
+    doc,
+    content='exports',
+    content_rowid='id'
+);
+
+-- FTS5 for file summaries (semantic intent search)
+CREATE VIRTUAL TABLE IF NOT EXISTS files_fts USING fts5(
+    path,
+    summary,
+    content='files',
+    content_rowid='rowid'
+);
+
+-- FTS5 for full file content (Smart Grep)
+CREATE VIRTUAL TABLE IF NOT EXISTS content_fts USING fts5(
+    file_path,
+    content,
+    content='file_content',
+    content_rowid='rowid'
+);
+
+-- Triggers to keep exports_fts in sync
+CREATE TRIGGER IF NOT EXISTS exports_ai AFTER INSERT ON exports BEGIN
+    INSERT INTO exports_fts(rowid, name, signature, doc)
+    VALUES (new.id, new.name, new.signature, new.doc);
+END;
+
+CREATE TRIGGER IF NOT EXISTS exports_ad AFTER DELETE ON exports BEGIN
+    INSERT INTO exports_fts(exports_fts, rowid, name, signature, doc)
+    VALUES('delete', old.id, old.name, old.signature, old.doc);
+END;
+
+CREATE TRIGGER IF NOT EXISTS exports_au AFTER UPDATE ON exports BEGIN
+    INSERT INTO exports_fts(exports_fts, rowid, name, signature, doc)
+    VALUES('delete', old.id, old.name, old.signature, old.doc);
+    INSERT INTO exports_fts(rowid, name, signature, doc)
+    VALUES (new.id, new.name, new.signature, new.doc);
+END;
+
+-- Triggers to keep files_fts in sync
+CREATE TRIGGER IF NOT EXISTS files_ai AFTER INSERT ON files BEGIN
+    INSERT INTO files_fts(rowid, path, summary)
+    VALUES (new.rowid, new.path, new.summary);
+END;
+
+CREATE TRIGGER IF NOT EXISTS files_ad AFTER DELETE ON files BEGIN
+    INSERT INTO files_fts(files_fts, rowid, path, summary)
+    VALUES('delete', old.rowid, old.path, old.summary);
+END;
+
+CREATE TRIGGER IF NOT EXISTS files_au AFTER UPDATE ON files BEGIN
+    INSERT INTO files_fts(files_fts, rowid, path, summary)
+    VALUES('delete', old.rowid, old.path, old.summary);
+    INSERT INTO files_fts(rowid, path, summary)
+    VALUES (new.rowid, new.path, new.summary);
+END;
+
+-- Triggers to keep content_fts in sync
+CREATE TRIGGER IF NOT EXISTS content_ai AFTER INSERT ON file_content BEGIN
+    INSERT INTO content_fts(rowid, file_path, content)
+    VALUES (new.rowid, new.file_path, new.content);
+END;
+
+CREATE TRIGGER IF NOT EXISTS content_ad AFTER DELETE ON file_content BEGIN
+    INSERT INTO content_fts(content_fts, rowid, file_path, content)
+    VALUES('delete', old.rowid, old.file_path, old.content);
+END;
+
+CREATE TRIGGER IF NOT EXISTS content_au AFTER UPDATE ON file_content BEGIN
+    INSERT INTO content_fts(content_fts, rowid, file_path, content)
+    VALUES('delete', old.rowid, old.file_path, old.content);
+    INSERT INTO content_fts(rowid, file_path, content)
+    VALUES (new.rowid, new.file_path, new.content);
+END;
+
+-- DOWN
+DROP TRIGGER IF EXISTS content_au;
+DROP TRIGGER IF EXISTS content_ad;
+DROP TRIGGER IF EXISTS content_ai;
+DROP TRIGGER IF EXISTS files_au;
+DROP TRIGGER IF EXISTS files_ad;
+DROP TRIGGER IF EXISTS files_ai;
+DROP TRIGGER IF EXISTS exports_au;
+DROP TRIGGER IF EXISTS exports_ad;
+DROP TRIGGER IF EXISTS exports_ai;
+DROP TABLE IF EXISTS content_fts;
+DROP TABLE IF EXISTS files_fts;
+DROP TABLE IF EXISTS exports_fts;

package/dist/data/migrations/003_mission_system.sql

@@ -0,0 +1,86 @@
+-- Mission tracking system (Cognitive Overlay)
+
+CREATE TABLE IF NOT EXISTS missions (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    name TEXT NOT NULL,
+    goal TEXT,
+    status TEXT DEFAULT 'planned',
+    strategy_graph TEXT,
+    git_branch TEXT,
+    commit_sha TEXT,
+    parent_id INTEGER,
+    verification_context TEXT,
+    outcome_contract TEXT,
+    created_at REAL DEFAULT (unixepoch()),
+    updated_at REAL DEFAULT (unixepoch()),
+    FOREIGN KEY(parent_id) REFERENCES missions(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS mission_artifacts (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    mission_id INTEGER NOT NULL,
+    type TEXT NOT NULL,
+    identifier TEXT NOT NULL,
+    metadata TEXT,
+    created_at INTEGER DEFAULT (unixepoch()),
+    FOREIGN KEY(mission_id) REFERENCES missions(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS intent_logs (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    mission_id INTEGER,
+    symbol_id INTEGER,
+    file_path TEXT,
+    type TEXT,
+    content TEXT,
+    confidence REAL DEFAULT 1.0,
+    symbol_name TEXT,
+    signature TEXT,
+    commit_sha TEXT,
+    created_at REAL DEFAULT (unixepoch()),
+    FOREIGN KEY(mission_id) REFERENCES missions(id) ON DELETE CASCADE,
+    FOREIGN KEY(symbol_id) REFERENCES exports(id) ON DELETE SET NULL,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS working_set (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    mission_id INTEGER,
+    file_path TEXT,
+    symbol_id INTEGER,
+    type TEXT,
+    created_at REAL DEFAULT (unixepoch()),
+    FOREIGN KEY(mission_id) REFERENCES missions(id) ON DELETE CASCADE,
+    FOREIGN KEY(file_path) REFERENCES files(path) ON DELETE CASCADE,
+    FOREIGN KEY(symbol_id) REFERENCES exports(id) ON DELETE CASCADE
+);
+
+CREATE TABLE IF NOT EXISTS cross_repo_links (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    mission_id INTEGER NOT NULL,
+    linked_repo_path TEXT NOT NULL,
+    linked_mission_id INTEGER NOT NULL,
+    relationship TEXT,
+    direction TEXT,
+    created_at REAL DEFAULT (unixepoch()),
+    FOREIGN KEY(mission_id) REFERENCES missions(id) ON DELETE CASCADE
+);
+
+-- Indexes
+CREATE INDEX IF NOT EXISTS idx_intent_mission ON intent_logs(mission_id);
+CREATE INDEX IF NOT EXISTS idx_intent_symbol ON intent_logs(symbol_id);
+CREATE INDEX IF NOT EXISTS idx_working_set_mission ON working_set(mission_id);
+CREATE INDEX IF NOT EXISTS idx_cross_repo_mission ON cross_repo_links(mission_id);
+CREATE INDEX IF NOT EXISTS idx_mission_artifacts_mission ON mission_artifacts(mission_id);
+
+-- DOWN
+DROP INDEX IF EXISTS idx_mission_artifacts_mission;
+DROP INDEX IF EXISTS idx_cross_repo_mission;
+DROP INDEX IF EXISTS idx_working_set_mission;
+DROP INDEX IF EXISTS idx_intent_symbol;
+DROP INDEX IF EXISTS idx_intent_mission;
+DROP TABLE IF EXISTS cross_repo_links;
+DROP TABLE IF EXISTS working_set;
+DROP TABLE IF EXISTS intent_logs;
+DROP TABLE IF EXISTS mission_artifacts;
+DROP TABLE IF EXISTS missions;

package/dist/data/migrations/004_event_mesh.sql

@@ -0,0 +1,17 @@
+-- UP
+CREATE TABLE IF NOT EXISTS event_synapses (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    type TEXT NOT NULL, -- 'socket_event' or 'api_route'
+    name TEXT NOT NULL, -- The string contract (e.g., 'user:created' or '/api/users')
+    direction TEXT NOT NULL, -- 'produce' or 'consume'
+    file_path TEXT NOT NULL,
+    line_number INTEGER,
+    code_snippet TEXT,
+    created_at REAL DEFAULT (unixepoch())
+);
+
+CREATE INDEX IF NOT EXISTS idx_events_name ON event_synapses(name);
+CREATE INDEX IF NOT EXISTS idx_events_file ON event_synapses(file_path);
+
+-- DOWN
+DROP TABLE IF EXISTS event_synapses;

package/dist/data/migrations/005_index_metadata.sql

@@ -0,0 +1,15 @@
+-- Add metadata table to track index completion status
+
+CREATE TABLE IF NOT EXISTS index_metadata (
+    key TEXT PRIMARY KEY,
+    value TEXT,
+    updated_at REAL DEFAULT (unixepoch())
+);
+
+-- Insert initial indexing state marker
+INSERT OR IGNORE INTO index_metadata (key, value) VALUES ('index_completed', 'false');
+INSERT OR IGNORE INTO index_metadata (key, value) VALUES ('index_version', '1');
+INSERT OR IGNORE INTO index_metadata (key, value) VALUES ('last_indexed_at', NULL);
+
+-- DOWN
+DROP TABLE IF EXISTS index_metadata;