@memberjunction/db-auto-doc 5.13.0 → 5.15.0

package/README.md

@@ -94,6 +94,43 @@ npm install @memberjunction/db-auto-doc
 npm install @memberjunction/db-auto-doc --save
 ```
 
+
+## Benchmark Results
+
+DBAutoDoc has been extensively benchmarked across multiple databases and LLM providers. Full details in the [research paper](research/v1/paper.md).
+
+### AdventureWorks2022 (71 tables, all constraints stripped)
+
+| Model Configuration | PK F1 | FK F1 | Overall |
+|---------------------|-------|-------|---------|
+| Gemini 3 Flash / 3.1 Pro | 95.0% | 94.2% | 96.1% (A+) |
+| Claude Sonnet 4.6 / Opus 4.6 | 95.0% | 93.0% | 96.1% (A+) |
+| GPT-5.4-mini / GPT-5.4 | 89.4% | 77.9% | 87.9% (B+) |
+
+### Cross-Database Results (Gemini Flash)
+
+| Database | Tables | PK F1 | FK F1 | Descriptions |
+|----------|--------|-------|-------|-------------|
+| AdventureWorks | 71 | 95.0% | 94.2% | 99% |
+| Chinook | 11 | 95.2% | 95.2% | 100% |
+| LousyDB (dark DB) | 20 | 97.6% | 77.2% | 100% |
+| Northwind | 13 | 72.7% | 75.0% | 100% |
+
+### Key Discovery Pipeline
+
+DBAutoDoc uses a 4-phase pipeline for relationship discovery:
+
+1. **Statistical Discovery** — PK/FK candidates via uniqueness analysis, value overlap, cardinality ratios. Six deterministic gates filter false positives with zero correct-key loss.
+2. **LLM Iterative Analysis** — The LLM creates new FK/PK proposals based on semantic understanding (89% precision on LLM-created FKs). Cross-table statistics provided in prompt context.
+3. **Ground Truth Locking** — High-confidence keys (≥90%) become immutable to protect correct discoveries.
+4. **Two-Pass Pruning** — A stronger model evaluates remaining candidates per-table, then holistically reviews all proposals.
+
+### Research Paper
+
+See [research/v1/](research/v1/) for the full paper, benchmark results, and comparison scripts:
+- **[Paper](research/v1/paper.md)** — "DBAutoDoc: Automated Discovery and Documentation of Undocumented Database Schemas via Statistical Analysis and Iterative LLM Refinement"
+- **[Results](research/v1/results/)** — Full exports (HTML, Markdown, ERD, SQL, CSV) for all public benchmarks
+
 ## Quick Start
 
 ### 1. Initialize
@@ -219,7 +256,7 @@ Generate SQL
   - Custom value - Generate queries for top N tables
 
 - **`tokenBudget`**: Controls LLM token usage and cost
-  - `100000` (default) - Limit to 100K tokens (~$0.50-1.00 with GPT-4o)
+  - `100000` (default) - Limit to 100K tokens (~$0.50-1.00 with Gemini Flash)
   - `0` - **Unlimited** token budget (useful with `maxTables: 0`)
   - Custom value - Set specific token limit for cost control
 
@@ -249,11 +286,11 @@ Generate SQL
 }
 ```
 
-**Model Recommendations:**
-- ✅ **GPT-4o** - Best balance of speed, cost, and quality (~$6-10 for 50 tables)
-- ✅ **Claude 3.5 Sonnet** - High quality, good reasoning about alignment
-- ⚠️ **GPT-5** - Very slow (reasoning model), doesn't support JSON format, expensive
-- ⚠️ **Groq** - Fast and cheap but may struggle with complex alignment
+**Model Recommendations (based on benchmark results):**
+- ✅ **Gemini 3 Flash** — Best overall: 96.1% (A+) on AdventureWorks, 1M context window, lowest cost (~$0.50/100 tables). Recommended default.
+- ✅ **Claude Sonnet 4.6** — Highest token efficiency: 96.1% (A+) with only 471K tokens, 100% description coverage. Best quality-per-token.
+- ⚠️ **GPT-5.4-mini** — Good but limited: 87.9% (B+), 272K context window causes FK misses on large tables.
+- 💡 **For pruning**: Use a stronger model (Gemini 3.1 Pro, Claude Opus 4.6, or GPT-5.4) via `modelOverrides` config for the precision-critical pruning pass.
 
 ### 4. Export
 
@@ -498,14 +535,69 @@ Tables and columns marked `userApproved: true` (via ground truth or manual appro
 Resume analysis with fine-grained control:
 
 ```bash
+# Resume from a previous run's state file
+db-auto-doc analyze --resume ./output/run-1/state.json
+
 # Resume and re-analyze tables with confidence below 70%
-db-auto-doc analyze --resume ./state.json --reanalyze-below-confidence 0.7
+db-auto-doc analyze --resume ./state.json --reanalyze-below 0.7
 
 # Resume with a different iteration limit
 db-auto-doc analyze --resume ./state.json --max-iterations 20
+
+# Resume with additional iterations (e.g., ran 5 originally, now want 3 more)
+db-auto-doc analyze --resume ./state.json --max-iterations 3
+```
+
+The `--reanalyze-below` flag clears `userApproved` on non-ground-truth tables whose latest confidence is below the threshold, allowing them to be re-analyzed while protecting authoritative descriptions.
+
+### Pruning-Only Mode
+
+Run just the FK pruning pass on an existing state file, skipping discovery and analysis iterations. Useful when you want to apply a stronger model to clean up FK false positives without re-running the full analysis:
+
+```bash
+# Run only the FK pruning pass on an existing state
+db-auto-doc analyze --resume ./output/run-1/state.json --pruning-only
+
+# Combine with a config that specifies a stronger pruning model
+db-auto-doc analyze --resume ./output/run-1/state.json --pruning-only --config ./config-with-pro-pruning.json
+```
+
+Requires `--resume` pointing to a state file that has already completed discovery and at least one analysis iteration. The pruning pass uses the `ai.modelOverrides.fkPruning` config to select a potentially stronger model (e.g., Gemini Pro, Claude Opus) for the precision-critical FK filtering.
+
+### CLI Flags Reference
+
+| Flag | Short | Description |
+|------|-------|-------------|
+| `--config` | `-c` | Path to config file (default: `./config.json`) |
+| `--resume` | `-r` | Resume from an existing state file |
+| `--max-iterations` | `-n` | Override max iterations from config |
+| `--reanalyze-below` | | Re-analyze tables with confidence below threshold (0-1) |
+| `--pruning-only` | | Skip discovery/iterations, run only PK/FK pruning (requires `--resume`) |
+
+
+### Standalone Pruning Command
+
+The `prune` command runs PK/FK pruning on an existing state file without re-running analysis. It provides interactive confirmation before applying changes.
+
+```bash
+# Interactive mode (shows proposals, asks for confirmation)
+db-auto-doc prune --state ./output/run-1/state.json --config ./config.json
+
+# Silent mode (applies all pruning automatically)
+db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --silent
+
+# PK-only or FK-only pruning
+db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --pk-only
+db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --fk-only
 ```
 
-The `--reanalyze-below-confidence` flag clears `userApproved` on non-ground-truth tables whose latest confidence is below the threshold, allowing them to be re-analyzed while protecting authoritative descriptions.
+| Flag | Description |
+|------|-------------|
+| `--state` | Path to existing state.json file (required) |
+| `--config` | Path to config file with AI settings (required) |
+| `--silent` | Skip interactive confirmation |
+| `--pk-only` | Only prune primary keys |
+| `--fk-only` | Only prune foreign keys |
 
 ### CodeGen Integration (Additional Schema Info)
 
@@ -632,7 +724,7 @@ This rich context enables AI to make accurate inferences.
   },
   "ai": {
     "provider": "openai",
-    "model": "gpt-4-turbo-preview",
+    "model": "gpt-5.4-mini",
     "apiKey": "sk-...",
     "temperature": 0.1,
     "maxTokens": 8000,
@@ -757,7 +849,7 @@ This rich context enables AI to make accurate inferences.
   },
   "ai": {
     "provider": "openai",
-    "model": "gpt-4-turbo-preview",
+    "model": "gpt-5.4-mini",
     "apiKey": "sk-...",
     "temperature": 0.1,
     "maxTokens": 8000
@@ -798,7 +890,7 @@ This rich context enables AI to make accurate inferences.
   },
   "ai": {
     "provider": "openai",
-    "model": "gpt-4-turbo-preview",
+    "model": "gpt-5.4-mini",
     "apiKey": "sk-...",
     "temperature": 0.1,
     "maxTokens": 8000
@@ -824,23 +916,71 @@ This rich context enables AI to make accurate inferences.
 }
 ```
 
+
+### Retry and Rate Limiting
+
+```json
+{
+  "ai": {
+    "retry": {
+      "maxRetries": 5,
+      "initialDelayMs": 30000,
+      "maxDelayMs": 480000,
+      "backoffMultiplier": 2
+    },
+    "rateLimits": {
+      "requestsPerMinute": 60,
+      "maxParallelRequests": 1
+    }
+  }
+}
+```
+
+Handles 429 (rate limit) and transient network errors with exponential backoff. Configure based on your API provider's limits.
+
+
+### Multi-Model Configuration
+
+Use different models for different pipeline phases. A cheaper/faster model for bulk analysis, a stronger model for precision-critical pruning:
+
+```json
+{
+  "ai": {
+    "provider": "gemini",
+    "model": "gemini-3-flash-preview",
+    "modelOverrides": {
+      "fkPruning": {
+        "model": "gemini-3.1-pro-preview",
+        "temperature": 0.05,
+        "maxTokens": 16000
+      },
+      "pkPruning": {
+        "model": "gemini-3.1-pro-preview",
+        "temperature": 0.05
+      }
+    }
+  }
+}
+```
+
+
 ## Supported AI Providers
 
-DBAutoDoc integrates with MemberJunction's AI provider system. Supported providers:
+DBAutoDoc integrates with [MemberJunction's AI provider system](../../packages/AI/). Supported providers:
 
 | Config Provider | Driver Class | Description |
 |-----------------|--------------|-------------|
-| `gemini` (default) | GeminiLLM | Google Gemini |
-| `openai` | OpenAILLM | OpenAI |
-| `anthropic` | AnthropicLLM | Anthropic Claude |
-| `groq` | GroqLLM | Groq |
-| `mistral` | MistralLLM | Mistral AI |
+| `gemini` (default) | [GeminiLLM](../../packages/AI/Providers/Gemini/) | Google Gemini |
+| `openai` | [OpenAILLM](../../packages/AI/Providers/OpenAI/) | OpenAI |
+| `anthropic` | [AnthropicLLM](../../packages/AI/Providers/Anthropic/) | Anthropic Claude |
+| `groq` | [GroqLLM](../../packages/AI/Providers/Groq/) | Groq |
+| `mistral` | [MistralLLM](../../packages/AI/Providers/Mistral/) | Mistral AI |
 | `vertex` | VertexLLM | Google Vertex AI |
 | `azure` | AzureLLM | Azure OpenAI |
-| `cerebras` | CerebrasLLM | Cerebras |
-| `openrouter` | OpenRouterLLM | OpenRouter (multi-model) |
-| `xai` | xAILLM | xAI (Grok) |
-| `bedrock` | BedrockLLM | AWS Bedrock |
+| `cerebras` | [CerebrasLLM](../../packages/AI/Providers/Cerebras/) | Cerebras |
+| `openrouter` | [OpenRouterLLM](../../packages/AI/Providers/OpenRouter/) | OpenRouter (multi-model) |
+| `xai` | [xAILLM](../../packages/AI/Providers/xAI/) | xAI (Grok) |
+| `bedrock` | [BedrockLLM](../../packages/AI/Providers/Bedrock/) | AWS Bedrock |
 
 ### Gemini (Default)
 ```json
@@ -855,7 +995,7 @@ DBAutoDoc integrates with MemberJunction's AI provider system. Supported provide
 ```json
 {
   "provider": "openai",
-  "model": "gpt-4-turbo-preview",
+  "model": "gpt-5.4-mini",
   "apiKey": "sk-..."
 }
 ```
@@ -864,7 +1004,7 @@ DBAutoDoc integrates with MemberJunction's AI provider system. Supported provide
 ```json
 {
   "provider": "anthropic",
-  "model": "claude-3-5-sonnet-20241022",
+  "model": "claude-sonnet-4-6",
   "apiKey": "sk-ant-..."
 }
 ```
@@ -873,7 +1013,7 @@ DBAutoDoc integrates with MemberJunction's AI provider system. Supported provide
 ```json
 {
   "provider": "groq",
-  "model": "llama-3.3-70b-versatile",
+  "model": "llama-4-scout-17b-16e-instruct",
   "apiKey": "gsk_..."
 }
 ```
@@ -1050,7 +1190,7 @@ const schemaInfo = schemaInfoGen.generate(state, {
 
 Typical costs (will vary by database size and complexity):
 
-| Database Size | Tables | Iterations | Tokens | Cost (GPT-4) | Cost (Groq) |
+| Database Size | Tables | Iterations | Tokens | Cost (Gemini Flash) | Cost (Sonnet 4.6) |
 |---------------|--------|------------|--------|--------------|-------------|
 | Small | 10-20 | 2-3 | ~50K | $0.50 | $0.02 |
 | Medium | 50-100 | 3-5 | ~200K | $2.00 | $0.08 |
@@ -1059,7 +1199,7 @@ Typical costs (will vary by database size and complexity):
 
 **With Relationship Discovery**: Add 25-40% to token/cost estimates for databases with missing constraints.
 
-**With Sample Query Generation** (5 queries/table, GPT-4o):
+**With Sample Query Generation** (5 queries/table, Gemini Flash):
 
 | Database Size | Tables | Additional Tokens | Additional Cost |
 |---------------|--------|-------------------|-----------------|
@@ -1081,13 +1221,13 @@ Note: Sample query generation uses ~6× more API calls than description generati
 6. **Filter exports** - Use `--confidence-threshold` to only apply high-confidence descriptions
 7. **Iterate** - Run analysis multiple times if first pass isn't satisfactory
 8. **Resume from checkpoints** - Save costs by continuing previous runs
-9. **Use appropriate models** - Balance cost vs. quality (GPT-4 vs. Groq)
+9. **Use appropriate models** - Balance cost vs. quality (see benchmark results)
 10. **Export multiple formats** - HTML for browsing, CSV for analysis, SQL for database
 
 ### Sample Query Generation Best Practices
 
 **Configuration:**
-1. **Use GPT-4o or Claude 3.5** - Best balance of quality, speed, and cost
+1. **Use Gemini 3 Flash or Claude Sonnet 4.6** - Best balance of quality, speed, and cost (see benchmark results)
 2. **Set token budget** - Prevents runaway costs (default: 100K tokens)
 3. **Start with 5 queries/table** - Good balance of coverage and cost
 4. **Enable query fix** (`enableQueryFix: true`, default) - Auto-fixes broken queries (up to 3 attempts)
@@ -1134,7 +1274,7 @@ Note: Sample query generation uses ~6× more API calls than description generati
 - Enable guardrails with appropriate limits
 - Reduce `maxTokens` per prompt
 - Filter schemas/tables to focus on subset
-- Use cheaper model (Groq instead of GPT-4)
+- Use cheaper model (Gemini Flash is already very cost-effective)
 - Disable relationship discovery if not needed
 
 ### "Guardrail limits exceeded"

package/bin/run.js

@@ -10,7 +10,7 @@ dotenvConfig({ path: resolve(__dirname, '../../../.env') });
 dotenvConfig();
 
 // Commands that need the full MJ server bootstrap (database connectivity, AI providers, etc.)
-const heavyCommands = ['analyze', 'generate-queries', 'export-sample-queries'];
+const heavyCommands = ['analyze', 'generate-queries', 'export-sample-queries', 'prune'];
 const commandArg = process.argv[2];
 const needsBootstrap = heavyCommands.includes(commandArg);
 

package/dist/commands/analyze.d.ts

@@ -8,6 +8,9 @@ export default class Analyze extends Command {
     static flags: {
         resume: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
         config: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'max-iterations': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<number, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'reanalyze-below': import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        'pruning-only': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
     };
     static args: {};
     run(): Promise<void>;

package/dist/commands/analyze.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"analyze.d.ts","sourceRoot":"","sources":["../../src/commands/analyze.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAS,MAAM,aAAa,CAAC;AAM7C,MAAM,CAAC,OAAO,OAAO,OAAQ,SAAQ,OAAO;IAC1C,MAAM,CAAC,WAAW,SAAiD;IAEnE,MAAM,CAAC,QAAQ,WAIb;IAEF,MAAM,CAAC,KAAK;;;MAWV;IAEF,MAAM,CAAC,IAAI,KAAM;IAEX,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAoD3B"}
+{"version":3,"file":"analyze.d.ts","sourceRoot":"","sources":["../../src/commands/analyze.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAS,MAAM,aAAa,CAAC;AAM7C,MAAM,CAAC,OAAO,OAAO,OAAQ,SAAQ,OAAO;IAC1C,MAAM,CAAC,WAAW,SAAiD;IAEnE,MAAM,CAAC,QAAQ,WAOb;IAEF,MAAM,CAAC,KAAK;;;;;;MAwBV;IAEF,MAAM,CAAC,IAAI,KAAM;IAEX,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC;CAqE3B"}

package/dist/commands/analyze.js

@@ -10,34 +10,64 @@ export default class Analyze extends Command {
     static { this.description = 'Analyze database and generate documentation'; }
     static { this.examples = [
         '$ db-auto-doc analyze',
-        '$ db-auto-doc analyze --resume ./output/run-6/state.json',
-        '$ db-auto-doc analyze --config ./my-config.json'
+        '$ db-auto-doc analyze --config ./my-config.json',
+        '$ db-auto-doc analyze --resume ./output/run-6/run-1/state.json',
+        '$ db-auto-doc analyze --resume ./output/run-6/run-1/state.json --max-iterations 3',
+        '$ db-auto-doc analyze --resume ./output/run-6/run-1/state.json --reanalyze-below 0.7',
+        '$ db-auto-doc analyze --resume ./output/run-6/run-1/state.json --pruning-only'
     ]; }
     static { this.flags = {
         resume: Flags.string({
             char: 'r',
-            description: 'Resume from an existing state file',
+            description: 'Resume from an existing state file. Skips schema introspection and discovery if state already has data.',
             required: false
         }),
         config: Flags.string({
             char: 'c',
             description: 'Path to config file',
             default: './config.json'
+        }),
+        'max-iterations': Flags.integer({
+            char: 'n',
+            description: 'Override max iterations from config for this run',
+            required: false
+        }),
+        'reanalyze-below': Flags.string({
+            description: 'Only re-analyze tables with confidence below this threshold (0-1). Use with --resume to refine low-confidence results.',
+            required: false
+        }),
+        'pruning-only': Flags.boolean({
+            description: 'Skip discovery and analysis iterations. Only run the FK pruning pass on an existing state file. Requires --resume.',
+            default: false
         })
     }; }
     static { this.args = {}; }
     async run() {
         const { flags } = await this.parse(Analyze);
         const spinner = ora();
+        // Validate flag combinations
+        if (flags['pruning-only'] && !flags.resume) {
+            this.error('--pruning-only requires --resume pointing to an existing state file');
+        }
         try {
             // Load configuration
             spinner.start('Loading configuration');
             const config = await ConfigLoader.load(flags.config);
             spinner.succeed('Configuration loaded');
+            // Parse reanalyze-below as number if provided
+            const reanalyzeBelowConfidence = flags['reanalyze-below'] != null
+                ? parseFloat(flags['reanalyze-below'])
+                : undefined;
+            // For pruning-only, set max iterations to 0 so iteration loop is skipped
+            const maxIterations = flags['pruning-only']
+                ? 0
+                : flags['max-iterations'];
             // Create orchestrator
             const orchestrator = new AnalysisOrchestrator({
                 config,
                 resumeFromState: flags.resume,
+                reanalyzeBelowConfidence,
+                maxIterations,
                 onProgress: (message, data) => {
                     if (data) {
                         spinner.succeed(`${message}: ${JSON.stringify(data)}`);

package/dist/commands/analyze.js.map

@@ -1 +1 @@
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package/dist/commands/prune.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Prune command - Standalone PK/FK pruning on existing state
+ */
+import { Command } from '@oclif/core';
+export default class Prune extends Command {
+    static description: string;
+    static examples: string[];
+    static flags: {
+        state: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        config: import("@oclif/core/lib/interfaces/parser.js").OptionFlag<string, import("@oclif/core/lib/interfaces/parser.js").CustomOptions>;
+        silent: import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'pk-only': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+        'fk-only': import("@oclif/core/lib/interfaces/parser.js").BooleanFlag<boolean>;
+    };
+    run(): Promise<void>;
+}
+//# sourceMappingURL=prune.d.ts.map

package/dist/commands/prune.d.ts.map

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package/dist/commands/prune.js

@@ -0,0 +1,153 @@
+/**
+ * Prune command - Standalone PK/FK pruning on existing state
+ */
+import { Command, Flags } from '@oclif/core';
+import ora from 'ora';
+import chalk from 'chalk';
+import * as fs from 'fs';
+import * as readline from 'readline';
+import { ConfigLoader } from '../utils/config-loader.js';
+import { AnalysisEngine } from '../core/AnalysisEngine.js';
+import { StateManager } from '../state/StateManager.js';
+import * as path from 'path';
+import { fileURLToPath } from 'node:url';
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+import { PromptEngine } from '../prompts/PromptEngine.js';
+import { IterationTracker } from '../state/IterationTracker.js';
+export default class Prune extends Command {
+    static { this.description = 'Run PK/FK pruning on an existing state file without re-running analysis'; }
+    static { this.examples = [
+        '$ db-auto-doc prune --state ./output/run-1/state.json --config ./config.json',
+        '$ db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --pk-only',
+        '$ db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --fk-only',
+        '$ db-auto-doc prune --state ./output/run-1/state.json --config ./config.json --silent'
+    ]; }
+    static { this.flags = {
+        state: Flags.string({
+            char: 's',
+            description: 'Path to existing state.json file',
+            required: true
+        }),
+        config: Flags.string({
+            char: 'c',
+            description: 'Path to config file',
+            default: './config.json'
+        }),
+        silent: Flags.boolean({
+            description: 'Skip interactive confirmation, apply all pruning proposals automatically',
+            default: false
+        }),
+        'pk-only': Flags.boolean({
+            description: 'Only prune primary keys',
+            default: false
+        }),
+        'fk-only': Flags.boolean({
+            description: 'Only prune foreign keys',
+            default: false
+        })
+    }; }
+    async run() {
+        const { flags } = await this.parse(Prune);
+        const spinner = ora();
+        try {
+            // Load config
+            spinner.start('Loading configuration');
+            const config = await ConfigLoader.load(flags.config);
+            spinner.succeed('Configuration loaded');
+            // Load state
+            spinner.start('Loading state file');
+            if (!fs.existsSync(flags.state)) {
+                this.error(`State file not found: ${flags.state}`);
+            }
+            const stateContent = fs.readFileSync(flags.state, 'utf-8');
+            const state = JSON.parse(stateContent);
+            spinner.succeed(`State loaded: ${state.schemas?.length || 0} schemas`);
+            // Create engine components
+            const stateManager = new StateManager(flags.state);
+            const promptsDir = path.join(__dirname, '../../prompts');
+            const promptEngine = new PromptEngine(config.ai, promptsDir);
+            const iterationTracker = new IterationTracker();
+            await promptEngine.initialize();
+            const analysisEngine = new AnalysisEngine(config, promptEngine, stateManager, iterationTracker);
+            // Create a minimal run object for tracking
+            const run = {
+                runId: 'prune-' + Date.now(),
+                startedAt: new Date().toISOString(),
+                status: 'in_progress',
+                levelsProcessed: 0,
+                iterationsPerformed: 0,
+                backpropagationCount: 0,
+                sanityCheckCount: 0,
+                converged: false,
+                modelUsed: config.ai.model,
+                vendor: config.ai.provider || 'gemini',
+                temperature: config.ai.temperature || 0.1,
+                totalTokensUsed: 0,
+                totalInputTokens: 0,
+                totalOutputTokens: 0,
+                estimatedCost: 0,
+                warnings: [],
+                errors: [],
+                processingLog: [],
+                sanityChecks: []
+            };
+            let pkResults = { removed: 0, kept: 0 };
+            let fkResults = { removed: 0, kept: 0 };
+            // PK pruning
+            if (!flags['fk-only'] && state.phases.keyDetection) {
+                spinner.start('Running PK pruning...');
+                const { locked: pkLocked, unlocked: pkUnlocked } = analysisEngine.lockInterimPKGroundTruth(state);
+                spinner.succeed(`PK ground truth: ${pkLocked} locked, ${pkUnlocked} unlocked`);
+                if (pkUnlocked > 0) {
+                    pkResults = await analysisEngine.prunePrimaryKeys(state, run);
+                    this.log(chalk.yellow(`  PK pruning: ${pkResults.removed} removed, ${pkResults.kept} kept`));
+                }
+                else {
+                    this.log(chalk.green('  No unlocked PKs to prune'));
+                }
+            }
+            // FK pruning
+            if (!flags['pk-only'] && state.phases.keyDetection) {
+                spinner.start('Running FK pruning...');
+                const { locked: fkLocked, unlocked: fkUnlocked } = analysisEngine.lockInterimGroundTruth(state);
+                spinner.succeed(`FK ground truth: ${fkLocked} locked, ${fkUnlocked} unlocked`);
+                if (fkUnlocked > 0) {
+                    fkResults = await analysisEngine.pruneForeignKeys(state, run);
+                    this.log(chalk.yellow(`  FK pruning: ${fkResults.removed} removed, ${fkResults.kept} kept`));
+                }
+                else {
+                    this.log(chalk.green('  No unlocked FKs to prune'));
+                }
+            }
+            // Summary
+            this.log('');
+            this.log(chalk.bold('Pruning Summary:'));
+            this.log(`  PKs: ${pkResults.removed} removed, ${pkResults.kept} kept`);
+            this.log(`  FKs: ${fkResults.removed} removed, ${fkResults.kept} kept`);
+            // Interactive confirmation (unless --silent)
+            if (!flags.silent && (pkResults.removed > 0 || fkResults.removed > 0)) {
+                const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
+                const answer = await new Promise(resolve => {
+                    rl.question(chalk.cyan('\nApply these changes? (Y/N): '), resolve);
+                });
+                rl.close();
+                if (answer.toLowerCase() !== 'y') {
+                    this.log(chalk.red('Changes discarded.'));
+                    return;
+                }
+            }
+            // Save updated state
+            spinner.start('Saving updated state');
+            stateManager.updateSummary(state);
+            fs.writeFileSync(flags.state, JSON.stringify(state, null, 2));
+            spinner.succeed(`State saved to ${flags.state}`);
+            this.log(chalk.green('\n✓ Pruning complete!'));
+        }
+        catch (error) {
+            spinner.fail('Pruning failed');
+            this.error(error.message);
+        }
+    }
+}
+//# sourceMappingURL=prune.js.map

package/dist/commands/prune.js.map

@@ -0,0 +1 @@
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