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<span class="md-ellipsis">
Claude Desktop (macOS)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#claude-desktop-windows" class="md-nav__link">
<span class="md-ellipsis">
Claude Desktop (Windows)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#vscode-with-mcp-extension" class="md-nav__link">
<span class="md-ellipsis">
VSCode with MCP Extension
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#configuration-profiles" class="md-nav__link">
<span class="md-ellipsis">
Configuration Profiles
</span>
</a>
<nav class="md-nav" aria-label="Configuration Profiles">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#profile-1-fast-decay-daily-memory" class="md-nav__link">
<span class="md-ellipsis">
Profile 1: Fast Decay (Daily Memory)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-2-standard-default" class="md-nav__link">
<span class="md-ellipsis">
Profile 2: Standard (Default)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-3-long-term-stm-weekly" class="md-nav__link">
<span class="md-ellipsis">
Profile 3: Long-Term STM (Weekly)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-4-with-embeddings" class="md-nav__link">
<span class="md-ellipsis">
Profile 4: With Embeddings
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#decay-model-configuration" class="md-nav__link">
<span class="md-ellipsis">
Decay Model Configuration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#storage-management" class="md-nav__link">
<span class="md-ellipsis">
Storage Management
</span>
</a>
<nav class="md-nav" aria-label="Storage Management">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#location" class="md-nav__link">
<span class="md-ellipsis">
Location
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#backup" class="md-nav__link">
<span class="md-ellipsis">
Backup
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#migration" class="md-nav__link">
<span class="md-ellipsis">
Migration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#reset-storage" class="md-nav__link">
<span class="md-ellipsis">
Reset Storage
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#integration-with-basic-memory" class="md-nav__link">
<span class="md-ellipsis">
Integration with Basic Memory
</span>
</a>
<nav class="md-nav" aria-label="Integration with Basic Memory">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#setup" class="md-nav__link">
<span class="md-ellipsis">
Setup
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#vault-structure" class="md-nav__link">
<span class="md-ellipsis">
Vault Structure
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#promotion-workflow" class="md-nav__link">
<span class="md-ellipsis">
Promotion Workflow
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#maintenance-tasks" class="md-nav__link">
<span class="md-ellipsis">
Maintenance Tasks
</span>
</a>
<nav class="md-nav" aria-label="Maintenance Tasks">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#maintenance-cli" class="md-nav__link">
<span class="md-ellipsis">
Maintenance CLI
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#daily-maintenance-automated" class="md-nav__link">
<span class="md-ellipsis">
Daily Maintenance (Automated)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#weekly-gc" class="md-nav__link">
<span class="md-ellipsis">
Weekly GC
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#monthly-review" class="md-nav__link">
<span class="md-ellipsis">
Monthly Review
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#monitoring" class="md-nav__link">
<span class="md-ellipsis">
Monitoring
</span>
</a>
<nav class="md-nav" aria-label="Monitoring">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#storage-stats" class="md-nav__link">
<span class="md-ellipsis">
Storage Stats
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#logs" class="md-nav__link">
<span class="md-ellipsis">
Logs
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#troubleshooting" class="md-nav__link">
<span class="md-ellipsis">
Troubleshooting
</span>
</a>
<nav class="md-nav" aria-label="Troubleshooting">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#server-wont-start" class="md-nav__link">
<span class="md-ellipsis">
Server won't start
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#embeddings-not-working" class="md-nav__link">
<span class="md-ellipsis">
Embeddings not working
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#promotion-fails" class="md-nav__link">
<span class="md-ellipsis">
Promotion fails
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#storage-issues" class="md-nav__link">
<span class="md-ellipsis">
Storage issues
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#performance-tuning" class="md-nav__link">
<span class="md-ellipsis">
Performance Tuning
</span>
</a>
<nav class="md-nav" aria-label="Performance Tuning">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#for-large-stores-5000-memories" class="md-nav__link">
<span class="md-ellipsis">
For Large Stores (> 5000 memories)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#for-semantic-search" class="md-nav__link">
<span class="md-ellipsis">
For Semantic Search
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#memory-usage" class="md-nav__link">
<span class="md-ellipsis">
Memory Usage
</span>
</a>
</li>
</ul>
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</li>
<li class="md-nav__item">
<a href="#security-considerations" class="md-nav__link">
<span class="md-ellipsis">
Security Considerations
</span>
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</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="../security/" class="md-nav__link">
<span class="md-ellipsis">
Security
</span>
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</li>
</ul>
</nav>
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<li class="md-nav__item md-nav__item--nested">
<input class="md-nav__toggle md-toggle md-toggle--indeterminate" type="checkbox" id="__nav_5" >
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<span class="md-ellipsis">
Development
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<span class="md-nav__icon md-icon"></span>
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Development
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<ul class="md-nav__list" data-md-scrollfix>
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<a href="../CONTRIBUTING/" class="md-nav__link">
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Contributing
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</li>
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<a href="../ROADMAP/" class="md-nav__link">
<span class="md-ellipsis">
Roadmap
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<a href="../future_roadmap/" class="md-nav__link">
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Future Plans
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<input class="md-nav__toggle md-toggle md-toggle--indeterminate" type="checkbox" id="__nav_6" >
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Features
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Features
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<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../features/auto-recall-conversation/" class="md-nav__link">
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Auto-Recall
</span>
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</li>
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<input class="md-nav__toggle md-toggle md-toggle--indeterminate" type="checkbox" id="__nav_7" >
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<span class="md-ellipsis">
About
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<nav class="md-nav" data-md-level="1" aria-labelledby="__nav_7_label" aria-expanded="false">
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About
</label>
<ul class="md-nav__list" data-md-scrollfix>
<li class="md-nav__item">
<a href="../LICENSE/" class="md-nav__link">
<span class="md-ellipsis">
License
</span>
</a>
</li>
<li class="md-nav__item">
<a href="../CHANGELOG/" class="md-nav__link">
<span class="md-ellipsis">
Changelog
</span>
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</li>
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</ul>
</nav>
</div>
</div>
</div>
<div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
<div class="md-sidebar__scrollwrap">
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<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
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Table of contents
</label>
<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
<li class="md-nav__item">
<a href="#production-installation-recommended" class="md-nav__link">
<span class="md-ellipsis">
Production Installation (Recommended)
</span>
</a>
<nav class="md-nav" aria-label="Production Installation (Recommended)">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#prerequisites" class="md-nav__link">
<span class="md-ellipsis">
Prerequisites
</span>
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</li>
<li class="md-nav__item">
<a href="#installation-options" class="md-nav__link">
<span class="md-ellipsis">
Installation Options
</span>
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</nav>
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<li class="md-nav__item">
<a href="#development-setup" class="md-nav__link">
<span class="md-ellipsis">
Development Setup
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<nav class="md-nav" aria-label="Development Setup">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#prerequisites_1" class="md-nav__link">
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Prerequisites
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#editable-installation" class="md-nav__link">
<span class="md-ellipsis">
Editable Installation
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<li class="md-nav__item">
<a href="#running-tests" class="md-nav__link">
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Running Tests
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<li class="md-nav__item">
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<span class="md-ellipsis">
MCP Integration
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<nav class="md-nav" aria-label="MCP Integration">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#claude-desktop-macos" class="md-nav__link">
<span class="md-ellipsis">
Claude Desktop (macOS)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#claude-desktop-windows" class="md-nav__link">
<span class="md-ellipsis">
Claude Desktop (Windows)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#vscode-with-mcp-extension" class="md-nav__link">
<span class="md-ellipsis">
VSCode with MCP Extension
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#configuration-profiles" class="md-nav__link">
<span class="md-ellipsis">
Configuration Profiles
</span>
</a>
<nav class="md-nav" aria-label="Configuration Profiles">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#profile-1-fast-decay-daily-memory" class="md-nav__link">
<span class="md-ellipsis">
Profile 1: Fast Decay (Daily Memory)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-2-standard-default" class="md-nav__link">
<span class="md-ellipsis">
Profile 2: Standard (Default)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-3-long-term-stm-weekly" class="md-nav__link">
<span class="md-ellipsis">
Profile 3: Long-Term STM (Weekly)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#profile-4-with-embeddings" class="md-nav__link">
<span class="md-ellipsis">
Profile 4: With Embeddings
</span>
</a>
</li>
</ul>
</nav>
</li>
<li class="md-nav__item">
<a href="#decay-model-configuration" class="md-nav__link">
<span class="md-ellipsis">
Decay Model Configuration
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#storage-management" class="md-nav__link">
<span class="md-ellipsis">
Storage Management
</span>
</a>
<nav class="md-nav" aria-label="Storage Management">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#location" class="md-nav__link">
<span class="md-ellipsis">
Location
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#backup" class="md-nav__link">
<span class="md-ellipsis">
Backup
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#migration" class="md-nav__link">
<span class="md-ellipsis">
Migration
</span>
</a>
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<li class="md-nav__item">
<a href="#reset-storage" class="md-nav__link">
<span class="md-ellipsis">
Reset Storage
</span>
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</li>
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<li class="md-nav__item">
<a href="#integration-with-basic-memory" class="md-nav__link">
<span class="md-ellipsis">
Integration with Basic Memory
</span>
</a>
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<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#setup" class="md-nav__link">
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Setup
</span>
</a>
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<a href="#vault-structure" class="md-nav__link">
<span class="md-ellipsis">
Vault Structure
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#promotion-workflow" class="md-nav__link">
<span class="md-ellipsis">
Promotion Workflow
</span>
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</li>
</ul>
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<a href="#maintenance-tasks" class="md-nav__link">
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Maintenance Tasks
</span>
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<nav class="md-nav" aria-label="Maintenance Tasks">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#maintenance-cli" class="md-nav__link">
<span class="md-ellipsis">
Maintenance CLI
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#daily-maintenance-automated" class="md-nav__link">
<span class="md-ellipsis">
Daily Maintenance (Automated)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#weekly-gc" class="md-nav__link">
<span class="md-ellipsis">
Weekly GC
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#monthly-review" class="md-nav__link">
<span class="md-ellipsis">
Monthly Review
</span>
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<a href="#monitoring" class="md-nav__link">
<span class="md-ellipsis">
Monitoring
</span>
</a>
<nav class="md-nav" aria-label="Monitoring">
<ul class="md-nav__list">
<li class="md-nav__item">
<a href="#storage-stats" class="md-nav__link">
<span class="md-ellipsis">
Storage Stats
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#logs" class="md-nav__link">
<span class="md-ellipsis">
Logs
</span>
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<li class="md-nav__item">
<a href="#troubleshooting" class="md-nav__link">
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Troubleshooting
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<a href="#server-wont-start" class="md-nav__link">
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Server won't start
</span>
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<li class="md-nav__item">
<a href="#embeddings-not-working" class="md-nav__link">
<span class="md-ellipsis">
Embeddings not working
</span>
</a>
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<li class="md-nav__item">
<a href="#promotion-fails" class="md-nav__link">
<span class="md-ellipsis">
Promotion fails
</span>
</a>
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<a href="#storage-issues" class="md-nav__link">
<span class="md-ellipsis">
Storage issues
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Performance Tuning
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<nav class="md-nav" aria-label="Performance Tuning">
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<li class="md-nav__item">
<a href="#for-large-stores-5000-memories" class="md-nav__link">
<span class="md-ellipsis">
For Large Stores (> 5000 memories)
</span>
</a>
</li>
<li class="md-nav__item">
<a href="#for-semantic-search" class="md-nav__link">
<span class="md-ellipsis">
For Semantic Search
</span>
</a>
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<a href="#memory-usage" class="md-nav__link">
<span class="md-ellipsis">
Memory Usage
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Security Considerations
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</div>
<div class="md-content" data-md-component="content">
<article class="md-content__inner md-typeset">
<a href="https://github.com/prefrontal-systems/cortexgraph/edit/main/docs/deployment.md" title="Edit this page" class="md-content__button md-icon" rel="edit">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M10 20H6V4h7v5h5v3.1l2-2V8l-6-6H6c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h4zm10.2-7c.1 0 .3.1.4.2l1.3 1.3c.2.2.2.6 0 .8l-1 1-2.1-2.1 1-1c.1-.1.2-.2.4-.2m0 3.9L14.1 23H12v-2.1l6.1-6.1z"/></svg>
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<h1 id="deployment-guide">Deployment Guide<a class="headerlink" href="#deployment-guide" title="Permanent link">¶</a></h1>
<h2 id="production-installation-recommended">Production Installation (Recommended)<a class="headerlink" href="#production-installation-recommended" title="Permanent link">¶</a></h2>
<h3 id="prerequisites">Prerequisites<a class="headerlink" href="#prerequisites" title="Permanent link">¶</a></h3>
<ul>
<li>Python 3.10+</li>
<li><code>uv</code> package manager</li>
</ul>
<h3 id="installation-options">Installation Options<a class="headerlink" href="#installation-options" title="Permanent link">¶</a></h3>
<p><strong>Recommended: UV Tool Install from PyPI</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a><span class="c1"># Install from PyPI (recommended - fast, isolated, automatic updates)</span>
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>uv<span class="w"> </span>tool<span class="w"> </span>install<span class="w"> </span>cortexgraph
</code></pre></div>
<p><strong>Alternative Methods:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="c1"># Using pipx (similar isolation, cross-platform)</span>
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>pipx<span class="w"> </span>install<span class="w"> </span>cortexgraph
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a>
<a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a><span class="c1"># Using pip (traditional, installs in current environment)</span>
<a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a>pip<span class="w"> </span>install<span class="w"> </span>cortexgraph
<a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a>
<a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a><span class="c1"># From GitHub (latest development version)</span>
<a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a>uv<span class="w"> </span>tool<span class="w"> </span>install<span class="w"> </span>git+https://github.com/prefrontal-systems/cortexgraph.git
</code></pre></div>
<p>All methods install <code>cortexgraph</code> and all 7 CLI commands. Configuration goes in <code>~/.config/cortexgraph/.env</code>.</p>
<hr />
<h2 id="development-setup">Development Setup<a class="headerlink" href="#development-setup" title="Permanent link">¶</a></h2>
<h3 id="prerequisites_1">Prerequisites<a class="headerlink" href="#prerequisites_1" title="Permanent link">¶</a></h3>
<ul>
<li>Python 3.10+</li>
<li><code>uv</code> (recommended) or <code>pip</code></li>
<li>Git</li>
</ul>
<h3 id="editable-installation">Editable Installation<a class="headerlink" href="#editable-installation" title="Permanent link">¶</a></h3>
<p><strong>For development only:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="c1"># Clone the repository</span>
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/prefrontal-systems/cortexgraph.git
<a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a><span class="nb">cd</span><span class="w"> </span>cortexgraph
<a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a>
<a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a><span class="c1"># Install with uv (recommended)</span>
<a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a>uv<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span><span class="s2">".[dev]"</span>
<a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a>
<a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a><span class="c1"># Or with pip</span>
<a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span><span class="s2">".[dev]"</span>
<a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a>
<a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a><span class="c1"># Copy environment template</span>
<a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a>cp<span class="w"> </span>.env.example<span class="w"> </span>.env
<a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>
<a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a><span class="c1"># Edit .env with your settings</span>
<a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>vim<span class="w"> </span>.env
</code></pre></div>
<h3 id="running-tests">Running Tests<a class="headerlink" href="#running-tests" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="c1"># Run all tests</span>
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>pytest
<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>
<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="c1"># With coverage</span>
<a id="__codelineno-3-5" name="__codelineno-3-5" href="#__codelineno-3-5"></a>pytest<span class="w"> </span>--cov<span class="o">=</span>cortexgraph<span class="w"> </span>--cov-report<span class="o">=</span>html
<a id="__codelineno-3-6" name="__codelineno-3-6" href="#__codelineno-3-6"></a>
<a id="__codelineno-3-7" name="__codelineno-3-7" href="#__codelineno-3-7"></a><span class="c1"># Run specific test file</span>
<a id="__codelineno-3-8" name="__codelineno-3-8" href="#__codelineno-3-8"></a>pytest<span class="w"> </span>tests/test_decay.py
<a id="__codelineno-3-9" name="__codelineno-3-9" href="#__codelineno-3-9"></a>
<a id="__codelineno-3-10" name="__codelineno-3-10" href="#__codelineno-3-10"></a><span class="c1"># Run with verbose output</span>
<a id="__codelineno-3-11" name="__codelineno-3-11" href="#__codelineno-3-11"></a>pytest<span class="w"> </span>-v
</code></pre></div>
<hr />
<h2 id="mcp-integration">MCP Integration<a class="headerlink" href="#mcp-integration" title="Permanent link">¶</a></h2>
<h3 id="claude-desktop-macos">Claude Desktop (macOS)<a class="headerlink" href="#claude-desktop-macos" title="Permanent link">¶</a></h3>
<p>Configuration file location:
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>~/Library/Application Support/Claude/claude_desktop_config.json
</code></pre></div></p>
<p><strong>For UV tool install (recommended):</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a><span class="p">{</span>
<a id="__codelineno-5-2" name="__codelineno-5-2" href="#__codelineno-5-2"></a><span class="w"> </span><span class="nt">"mcpServers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-5-3" name="__codelineno-5-3" href="#__codelineno-5-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-5-4" name="__codelineno-5-4" href="#__codelineno-5-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"cortexgraph"</span>
<a id="__codelineno-5-5" name="__codelineno-5-5" href="#__codelineno-5-5"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-5-6" name="__codelineno-5-6" href="#__codelineno-5-6"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-5-7" name="__codelineno-5-7" href="#__codelineno-5-7"></a><span class="p">}</span>
</code></pre></div>
<p><strong>For development (editable install):</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-6-1" name="__codelineno-6-1" href="#__codelineno-6-1"></a><span class="p">{</span>
<a id="__codelineno-6-2" name="__codelineno-6-2" href="#__codelineno-6-2"></a><span class="w"> </span><span class="nt">"mcpServers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-6-3" name="__codelineno-6-3" href="#__codelineno-6-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-6-4" name="__codelineno-6-4" href="#__codelineno-6-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"uv"</span><span class="p">,</span>
<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="w"> </span><span class="nt">"args"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="s2">"--directory"</span><span class="p">,</span><span class="w"> </span><span class="s2">"/path/to/cortexgraph"</span><span class="p">,</span><span class="w"> </span><span class="s2">"run"</span><span class="p">,</span><span class="w"> </span><span class="s2">"cortexgraph"</span><span class="p">],</span>
<a id="__codelineno-6-6" name="__codelineno-6-6" href="#__codelineno-6-6"></a><span class="w"> </span><span class="nt">"env"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="nt">"PYTHONPATH"</span><span class="p">:</span><span class="w"> </span><span class="s2">"/path/to/cortexgraph/src"</span><span class="p">}</span>
<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-6-8" name="__codelineno-6-8" href="#__codelineno-6-8"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-6-9" name="__codelineno-6-9" href="#__codelineno-6-9"></a><span class="p">}</span>
</code></pre></div>
<p><strong>Configuration:</strong> All settings go in <code>~/.config/cortexgraph/.env</code>, not in the MCP config. See <code>.env.example</code> for options.</p>
<p><strong>Troubleshooting: Command Not Found</strong></p>
<p>If Claude Desktop shows <code>spawn cortexgraph ENOENT</code> errors, the <code>cortexgraph</code> command isn't in Claude Desktop's PATH.</p>
<p>GUI applications on macOS/Linux don't inherit shell PATH configurations (<code>.zshrc</code>, <code>.bashrc</code>, etc.). Claude Desktop only searches:
- <code>/usr/local/bin</code>
- <code>/opt/homebrew/bin</code> (macOS)
- <code>/usr/bin</code>, <code>/bin</code>, <code>/usr/sbin</code>, <code>/sbin</code></p>
<p>If <code>uv tool install</code> placed <code>cortexgraph</code> in <code>~/.local/bin/</code> or another custom location, Claude Desktop can't find it.</p>
<p><strong>Solution: Use absolute path</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="c1"># Find where cortexgraph is installed</span>
<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></a>which<span class="w"> </span>cortexgraph
<a id="__codelineno-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></a><span class="c1"># Example output: /Users/username/.local/bin/cortexgraph</span>
</code></pre></div>
<p>Update Claude config with the absolute path:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="p">{</span>
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a><span class="w"> </span><span class="nt">"mcpServers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"/Users/username/.local/bin/cortexgraph"</span>
<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="p">}</span>
</code></pre></div>
<p><strong>Alternative: System-wide install</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-9-1" name="__codelineno-9-1" href="#__codelineno-9-1"></a><span class="c1"># Option 1: Symlink to system location</span>
<a id="__codelineno-9-2" name="__codelineno-9-2" href="#__codelineno-9-2"></a>sudo<span class="w"> </span>ln<span class="w"> </span>-s<span class="w"> </span>~/.local/bin/cortexgraph<span class="w"> </span>/usr/local/bin/cortexgraph
<a id="__codelineno-9-3" name="__codelineno-9-3" href="#__codelineno-9-3"></a>
<a id="__codelineno-9-4" name="__codelineno-9-4" href="#__codelineno-9-4"></a><span class="c1"># Option 2: Install with UV to system location (requires admin)</span>
<a id="__codelineno-9-5" name="__codelineno-9-5" href="#__codelineno-9-5"></a>sudo<span class="w"> </span>uv<span class="w"> </span>tool<span class="w"> </span>install<span class="w"> </span>git+https://github.com/prefrontal-systems/cortexgraph.git
</code></pre></div>
<p>Restart Claude Desktop after configuration.</p>
<h3 id="claude-desktop-windows">Claude Desktop (Windows)<a class="headerlink" href="#claude-desktop-windows" title="Permanent link">¶</a></h3>
<p>Configuration file location:
<div class="highlight"><pre><span></span><code><a id="__codelineno-10-1" name="__codelineno-10-1" href="#__codelineno-10-1"></a>%APPDATA%\Claude\claude_desktop_config.json
</code></pre></div></p>
<p><strong>For UV tool install:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-11-1" name="__codelineno-11-1" href="#__codelineno-11-1"></a><span class="p">{</span>
<a id="__codelineno-11-2" name="__codelineno-11-2" href="#__codelineno-11-2"></a><span class="w"> </span><span class="nt">"mcpServers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-11-3" name="__codelineno-11-3" href="#__codelineno-11-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-11-4" name="__codelineno-11-4" href="#__codelineno-11-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"cortexgraph"</span>
<a id="__codelineno-11-5" name="__codelineno-11-5" href="#__codelineno-11-5"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-11-6" name="__codelineno-11-6" href="#__codelineno-11-6"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-11-7" name="__codelineno-11-7" href="#__codelineno-11-7"></a><span class="p">}</span>
</code></pre></div>
<p><strong>For development:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-12-1" name="__codelineno-12-1" href="#__codelineno-12-1"></a><span class="p">{</span>
<a id="__codelineno-12-2" name="__codelineno-12-2" href="#__codelineno-12-2"></a><span class="w"> </span><span class="nt">"mcpServers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-12-3" name="__codelineno-12-3" href="#__codelineno-12-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-12-4" name="__codelineno-12-4" href="#__codelineno-12-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"uv"</span><span class="p">,</span>
<a id="__codelineno-12-5" name="__codelineno-12-5" href="#__codelineno-12-5"></a><span class="w"> </span><span class="nt">"args"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="s2">"--directory"</span><span class="p">,</span><span class="w"> </span><span class="s2">"C:\\path\\to\\cortexgraph"</span><span class="p">,</span><span class="w"> </span><span class="s2">"run"</span><span class="p">,</span><span class="w"> </span><span class="s2">"cortexgraph"</span><span class="p">],</span>
<a id="__codelineno-12-6" name="__codelineno-12-6" href="#__codelineno-12-6"></a><span class="w"> </span><span class="nt">"env"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="nt">"PYTHONPATH"</span><span class="p">:</span><span class="w"> </span><span class="s2">"C:\\path\\to\\cortexgraph\\src"</span><span class="p">}</span>
<a id="__codelineno-12-7" name="__codelineno-12-7" href="#__codelineno-12-7"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-12-8" name="__codelineno-12-8" href="#__codelineno-12-8"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-12-9" name="__codelineno-12-9" href="#__codelineno-12-9"></a><span class="p">}</span>
</code></pre></div>
<h3 id="vscode-with-mcp-extension">VSCode with MCP Extension<a class="headerlink" href="#vscode-with-mcp-extension" title="Permanent link">¶</a></h3>
<p><strong>For UV tool install:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-13-1" name="__codelineno-13-1" href="#__codelineno-13-1"></a><span class="p">{</span>
<a id="__codelineno-13-2" name="__codelineno-13-2" href="#__codelineno-13-2"></a><span class="w"> </span><span class="nt">"mcp.servers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-13-3" name="__codelineno-13-3" href="#__codelineno-13-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-13-4" name="__codelineno-13-4" href="#__codelineno-13-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"cortexgraph"</span>
<a id="__codelineno-13-5" name="__codelineno-13-5" href="#__codelineno-13-5"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-13-6" name="__codelineno-13-6" href="#__codelineno-13-6"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-13-7" name="__codelineno-13-7" href="#__codelineno-13-7"></a><span class="p">}</span>
</code></pre></div>
<p><strong>For development:</strong></p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-14-1" name="__codelineno-14-1" href="#__codelineno-14-1"></a><span class="p">{</span>
<a id="__codelineno-14-2" name="__codelineno-14-2" href="#__codelineno-14-2"></a><span class="w"> </span><span class="nt">"mcp.servers"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-14-3" name="__codelineno-14-3" href="#__codelineno-14-3"></a><span class="w"> </span><span class="nt">"cortexgraph"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span>
<a id="__codelineno-14-4" name="__codelineno-14-4" href="#__codelineno-14-4"></a><span class="w"> </span><span class="nt">"command"</span><span class="p">:</span><span class="w"> </span><span class="s2">"uv"</span><span class="p">,</span>
<a id="__codelineno-14-5" name="__codelineno-14-5" href="#__codelineno-14-5"></a><span class="w"> </span><span class="nt">"args"</span><span class="p">:</span><span class="w"> </span><span class="p">[</span><span class="s2">"--directory"</span><span class="p">,</span><span class="w"> </span><span class="s2">"${workspaceFolder}"</span><span class="p">,</span><span class="w"> </span><span class="s2">"run"</span><span class="p">,</span><span class="w"> </span><span class="s2">"cortexgraph"</span><span class="p">],</span>
<a id="__codelineno-14-6" name="__codelineno-14-6" href="#__codelineno-14-6"></a><span class="w"> </span><span class="nt">"env"</span><span class="p">:</span><span class="w"> </span><span class="p">{</span><span class="nt">"PYTHONPATH"</span><span class="p">:</span><span class="w"> </span><span class="s2">"${workspaceFolder}/src"</span><span class="p">}</span>
<a id="__codelineno-14-7" name="__codelineno-14-7" href="#__codelineno-14-7"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-14-8" name="__codelineno-14-8" href="#__codelineno-14-8"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-14-9" name="__codelineno-14-9" href="#__codelineno-14-9"></a><span class="p">}</span>
</code></pre></div>
<hr />
<h2 id="configuration-profiles">Configuration Profiles<a class="headerlink" href="#configuration-profiles" title="Permanent link">¶</a></h2>
<h3 id="profile-1-fast-decay-daily-memory">Profile 1: Fast Decay (Daily Memory)<a class="headerlink" href="#profile-1-fast-decay-daily-memory" title="Permanent link">¶</a></h3>
<p>Use for information that's only relevant for a day or two.</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-15-1" name="__codelineno-15-1" href="#__codelineno-15-1"></a><span class="c1"># .env</span>
<a id="__codelineno-15-2" name="__codelineno-15-2" href="#__codelineno-15-2"></a><span class="nv">CORTEXGRAPH_DECAY_LAMBDA</span><span class="o">=</span><span class="m">8</span>.02e-6<span class="w"> </span><span class="c1"># 1-day half-life</span>
<a id="__codelineno-15-3" name="__codelineno-15-3" href="#__codelineno-15-3"></a><span class="nv">CORTEXGRAPH_FORGET_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.03
<a id="__codelineno-15-4" name="__codelineno-15-4" href="#__codelineno-15-4"></a><span class="nv">CORTEXGRAPH_PROMOTE_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.7
<a id="__codelineno-15-5" name="__codelineno-15-5" href="#__codelineno-15-5"></a><span class="nv">CORTEXGRAPH_PROMOTE_USE_COUNT</span><span class="o">=</span><span class="m">3</span>
</code></pre></div>
<h3 id="profile-2-standard-default">Profile 2: Standard (Default)<a class="headerlink" href="#profile-2-standard-default" title="Permanent link">¶</a></h3>
<p>Balanced for general use.</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-16-1" name="__codelineno-16-1" href="#__codelineno-16-1"></a><span class="c1"># .env</span>
<a id="__codelineno-16-2" name="__codelineno-16-2" href="#__codelineno-16-2"></a><span class="nv">CORTEXGRAPH_DECAY_LAMBDA</span><span class="o">=</span><span class="m">2</span>.673e-6<span class="w"> </span><span class="c1"># 3-day half-life</span>
<a id="__codelineno-16-3" name="__codelineno-16-3" href="#__codelineno-16-3"></a><span class="nv">CORTEXGRAPH_FORGET_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.05
<a id="__codelineno-16-4" name="__codelineno-16-4" href="#__codelineno-16-4"></a><span class="nv">CORTEXGRAPH_PROMOTE_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.65
<a id="__codelineno-16-5" name="__codelineno-16-5" href="#__codelineno-16-5"></a><span class="nv">CORTEXGRAPH_PROMOTE_USE_COUNT</span><span class="o">=</span><span class="m">5</span>
</code></pre></div>
<h3 id="profile-3-long-term-stm-weekly">Profile 3: Long-Term STM (Weekly)<a class="headerlink" href="#profile-3-long-term-stm-weekly" title="Permanent link">¶</a></h3>
<p>For information that should persist longer.</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-17-1" name="__codelineno-17-1" href="#__codelineno-17-1"></a><span class="c1"># .env</span>
<a id="__codelineno-17-2" name="__codelineno-17-2" href="#__codelineno-17-2"></a><span class="nv">CORTEXGRAPH_DECAY_LAMBDA</span><span class="o">=</span><span class="m">1</span>.145e-6<span class="w"> </span><span class="c1"># 7-day half-life</span>
<a id="__codelineno-17-3" name="__codelineno-17-3" href="#__codelineno-17-3"></a><span class="nv">CORTEXGRAPH_FORGET_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.08
<a id="__codelineno-17-4" name="__codelineno-17-4" href="#__codelineno-17-4"></a><span class="nv">CORTEXGRAPH_PROMOTE_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.6
<a id="__codelineno-17-5" name="__codelineno-17-5" href="#__codelineno-17-5"></a><span class="nv">CORTEXGRAPH_PROMOTE_USE_COUNT</span><span class="o">=</span><span class="m">7</span>
</code></pre></div>
<h3 id="profile-4-with-embeddings">Profile 4: With Embeddings<a class="headerlink" href="#profile-4-with-embeddings" title="Permanent link">¶</a></h3>
<p>Enable semantic search and clustering.</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-18-1" name="__codelineno-18-1" href="#__codelineno-18-1"></a><span class="c1"># .env</span>
<a id="__codelineno-18-2" name="__codelineno-18-2" href="#__codelineno-18-2"></a><span class="nv">CORTEXGRAPH_ENABLE_EMBEDDINGS</span><span class="o">=</span><span class="nb">true</span>
<a id="__codelineno-18-3" name="__codelineno-18-3" href="#__codelineno-18-3"></a><span class="nv">CORTEXGRAPH_EMBED_MODEL</span><span class="o">=</span>all-MiniLM-L6-v2
<a id="__codelineno-18-4" name="__codelineno-18-4" href="#__codelineno-18-4"></a><span class="nv">CORTEXGRAPH_SEMANTIC_HI</span><span class="o">=</span><span class="m">0</span>.88
<a id="__codelineno-18-5" name="__codelineno-18-5" href="#__codelineno-18-5"></a><span class="nv">CORTEXGRAPH_SEMANTIC_LO</span><span class="o">=</span><span class="m">0</span>.78
<a id="__codelineno-18-6" name="__codelineno-18-6" href="#__codelineno-18-6"></a><span class="nv">CORTEXGRAPH_CLUSTER_LINK_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.83
</code></pre></div>
<p><strong>Note</strong>: First run will download the model (~50MB).</p>
<hr />
<h2 id="decay-model-configuration">Decay Model Configuration<a class="headerlink" href="#decay-model-configuration" title="Permanent link">¶</a></h2>
<p>Select decay behavior via <code>CORTEXGRAPH_DECAY_MODEL</code>:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-19-1" name="__codelineno-19-1" href="#__codelineno-19-1"></a><span class="c1"># 1) Power-Law (default; heavier tail, most human)</span>
<a id="__codelineno-19-2" name="__codelineno-19-2" href="#__codelineno-19-2"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>power_law
<a id="__codelineno-19-3" name="__codelineno-19-3" href="#__codelineno-19-3"></a><span class="nv">CORTEXGRAPH_PL_ALPHA</span><span class="o">=</span><span class="m">1</span>.1<span class="w"> </span><span class="c1"># shape (typical 1.0–1.2)</span>
<a id="__codelineno-19-4" name="__codelineno-19-4" href="#__codelineno-19-4"></a><span class="nv">CORTEXGRAPH_PL_HALFLIFE_DAYS</span><span class="o">=</span><span class="m">3</span>.0<span class="w"> </span><span class="c1"># target half-life used to derive t0</span>
<a id="__codelineno-19-5" name="__codelineno-19-5" href="#__codelineno-19-5"></a>
<a id="__codelineno-19-6" name="__codelineno-19-6" href="#__codelineno-19-6"></a><span class="c1"># 2) Exponential (lighter tail, forgets sooner)</span>
<a id="__codelineno-19-7" name="__codelineno-19-7" href="#__codelineno-19-7"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>exponential
<a id="__codelineno-19-8" name="__codelineno-19-8" href="#__codelineno-19-8"></a><span class="nv">CORTEXGRAPH_DECAY_LAMBDA</span><span class="o">=</span><span class="m">2</span>.673e-6<span class="w"> </span><span class="c1"># ~3-day half-life (ln(2)/(3*86400))</span>
<a id="__codelineno-19-9" name="__codelineno-19-9" href="#__codelineno-19-9"></a>
<a id="__codelineno-19-10" name="__codelineno-19-10" href="#__codelineno-19-10"></a><span class="c1"># 3) Two-Component (fast early forgetting + heavier tail)</span>
<a id="__codelineno-19-11" name="__codelineno-19-11" href="#__codelineno-19-11"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>two_component
<a id="__codelineno-19-12" name="__codelineno-19-12" href="#__codelineno-19-12"></a><span class="nv">CORTEXGRAPH_TC_LAMBDA_FAST</span><span class="o">=</span><span class="m">1</span>.603e-5<span class="w"> </span><span class="c1"># ~12-hour half-life</span>
<a id="__codelineno-19-13" name="__codelineno-19-13" href="#__codelineno-19-13"></a><span class="nv">CORTEXGRAPH_TC_LAMBDA_SLOW</span><span class="o">=</span><span class="m">1</span>.147e-6<span class="w"> </span><span class="c1"># ~7-day half-life</span>
<a id="__codelineno-19-14" name="__codelineno-19-14" href="#__codelineno-19-14"></a><span class="nv">CORTEXGRAPH_TC_WEIGHT_FAST</span><span class="o">=</span><span class="m">0</span>.7<span class="w"> </span><span class="c1"># weight of fast component (0–1)</span>
<a id="__codelineno-19-15" name="__codelineno-19-15" href="#__codelineno-19-15"></a>
<a id="__codelineno-19-16" name="__codelineno-19-16" href="#__codelineno-19-16"></a><span class="c1"># Shared parameters</span>
<a id="__codelineno-19-17" name="__codelineno-19-17" href="#__codelineno-19-17"></a><span class="nv">CORTEXGRAPH_DECAY_BETA</span><span class="o">=</span><span class="m">0</span>.6<span class="w"> </span><span class="c1"># sub-linear use count weight</span>
<a id="__codelineno-19-18" name="__codelineno-19-18" href="#__codelineno-19-18"></a><span class="nv">CORTEXGRAPH_FORGET_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.05<span class="w"> </span><span class="c1"># GC threshold</span>
<a id="__codelineno-19-19" name="__codelineno-19-19" href="#__codelineno-19-19"></a><span class="nv">CORTEXGRAPH_PROMOTE_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.65<span class="w"> </span><span class="c1"># promotion threshold</span>
<a id="__codelineno-19-20" name="__codelineno-19-20" href="#__codelineno-19-20"></a><span class="nv">CORTEXGRAPH_PROMOTE_USE_COUNT</span><span class="o">=</span><span class="m">5</span>
<a id="__codelineno-19-21" name="__codelineno-19-21" href="#__codelineno-19-21"></a><span class="nv">CORTEXGRAPH_PROMOTE_TIME_WINDOW</span><span class="o">=</span><span class="m">14</span>
</code></pre></div>
<p>Tuning tips:
- Power-Law has a heavier tail; consider a slightly higher <code>CORTEXGRAPH_FORGET_THRESHOLD</code> (e.g., 0.06–0.08) or reduce <code>CORTEXGRAPH_PL_HALFLIFE_DAYS</code> to maintain GC budget.
- Two-Component forgets very recent items faster; validate promotion and GC rates and adjust thresholds as needed.</p>
<hr />
<h2 id="storage-management">Storage Management<a class="headerlink" href="#storage-management" title="Permanent link">¶</a></h2>
<h3 id="location">Location<a class="headerlink" href="#location" title="Permanent link">¶</a></h3>
<p>Default directory: <code>~/.config/cortexgraph/jsonl/</code></p>
<p>Custom location via <code>CORTEXGRAPH_STORAGE_PATH</code> environment variable.</p>
<h3 id="backup">Backup<a class="headerlink" href="#backup" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-20-1" name="__codelineno-20-1" href="#__codelineno-20-1"></a><span class="c1"># Simple backup</span>
<a id="__codelineno-20-2" name="__codelineno-20-2" href="#__codelineno-20-2"></a>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/memories.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/memories.jsonl.backup
<a id="__codelineno-20-3" name="__codelineno-20-3" href="#__codelineno-20-3"></a>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/relations.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/relations.jsonl.backup
<a id="__codelineno-20-4" name="__codelineno-20-4" href="#__codelineno-20-4"></a>
<a id="__codelineno-20-5" name="__codelineno-20-5" href="#__codelineno-20-5"></a><span class="c1"># Timestamped backup</span>
<a id="__codelineno-20-6" name="__codelineno-20-6" href="#__codelineno-20-6"></a>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/memories.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/memories.jsonl.<span class="k">$(</span>date<span class="w"> </span>+%Y%m%d<span class="k">)</span>
<a id="__codelineno-20-7" name="__codelineno-20-7" href="#__codelineno-20-7"></a>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/relations.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/relations.jsonl.<span class="k">$(</span>date<span class="w"> </span>+%Y%m%d<span class="k">)</span>
<a id="__codelineno-20-8" name="__codelineno-20-8" href="#__codelineno-20-8"></a>
<a id="__codelineno-20-9" name="__codelineno-20-9" href="#__codelineno-20-9"></a><span class="c1"># Automated daily backup (cron)</span>
<a id="__codelineno-20-10" name="__codelineno-20-10" href="#__codelineno-20-10"></a><span class="m">0</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>*<span class="w"> </span>*<span class="w"> </span>*<span class="w"> </span>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/memories.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/memories.jsonl.<span class="k">$(</span>date<span class="w"> </span>+<span class="se">\%</span>Y<span class="se">\%</span>m<span class="se">\%</span>d<span class="k">)</span><span class="w"> </span><span class="o">&&</span><span class="w"> </span>cp<span class="w"> </span>~/.config/cortexgraph/jsonl/relations.jsonl<span class="w"> </span>~/.config/cortexgraph/backups/relations.jsonl.<span class="k">$(</span>date<span class="w"> </span>+<span class="se">\%</span>Y<span class="se">\%</span>m<span class="se">\%</span>d<span class="k">)</span>
</code></pre></div>
<h3 id="migration">Migration<a class="headerlink" href="#migration" title="Permanent link">¶</a></h3>
<p>Not applicable. JSONL storage requires no schema migrations.</p>
<h3 id="reset-storage">Reset Storage<a class="headerlink" href="#reset-storage" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-21-1" name="__codelineno-21-1" href="#__codelineno-21-1"></a><span class="c1"># WARNING: This deletes all memories</span>
<a id="__codelineno-21-2" name="__codelineno-21-2" href="#__codelineno-21-2"></a>rm<span class="w"> </span>-rf<span class="w"> </span>~/.config/cortexgraph/jsonl
<a id="__codelineno-21-3" name="__codelineno-21-3" href="#__codelineno-21-3"></a>
<a id="__codelineno-21-4" name="__codelineno-21-4" href="#__codelineno-21-4"></a><span class="c1"># Next run will create fresh storage files</span>
<a id="__codelineno-21-5" name="__codelineno-21-5" href="#__codelineno-21-5"></a>cortexgraph
</code></pre></div>
<hr />
<h2 id="integration-with-basic-memory">Integration with Basic Memory<a class="headerlink" href="#integration-with-basic-memory" title="Permanent link">¶</a></h2>
<h3 id="setup">Setup<a class="headerlink" href="#setup" title="Permanent link">¶</a></h3>
<ol>
<li>Configure Basic Memory MCP server</li>
<li>Set <code>BASIC_MEMORY_PATH</code> to your Obsidian vault</li>
<li>STM will create a <code>STM/</code> folder in the vault</li>
<li>Promoted memories appear as Markdown notes</li>
</ol>
<h3 id="vault-structure">Vault Structure<a class="headerlink" href="#vault-structure" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-22-1" name="__codelineno-22-1" href="#__codelineno-22-1"></a>Vault/
<a id="__codelineno-22-2" name="__codelineno-22-2" href="#__codelineno-22-2"></a>├── STM/
<a id="__codelineno-22-3" name="__codelineno-22-3" href="#__codelineno-22-3"></a>│ ├── memory-abc-123.md
<a id="__codelineno-22-4" name="__codelineno-22-4" href="#__codelineno-22-4"></a>│ ├── project-deadline.md
<a id="__codelineno-22-5" name="__codelineno-22-5" href="#__codelineno-22-5"></a>│ └── important-note.md
<a id="__codelineno-22-6" name="__codelineno-22-6" href="#__codelineno-22-6"></a>└── [other Basic Memory notes]
</code></pre></div>
<h3 id="promotion-workflow">Promotion Workflow<a class="headerlink" href="#promotion-workflow" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-23-1" name="__codelineno-23-1" href="#__codelineno-23-1"></a><span class="c1"># 1. Auto-detect promotion candidates</span>
<a id="__codelineno-23-2" name="__codelineno-23-2" href="#__codelineno-23-2"></a><span class="o">{</span>
<a id="__codelineno-23-3" name="__codelineno-23-3" href="#__codelineno-23-3"></a><span class="w"> </span><span class="s2">"auto_detect"</span>:<span class="w"> </span>true,
<a id="__codelineno-23-4" name="__codelineno-23-4" href="#__codelineno-23-4"></a><span class="w"> </span><span class="s2">"dry_run"</span>:<span class="w"> </span><span class="nb">true</span>
<a id="__codelineno-23-5" name="__codelineno-23-5" href="#__codelineno-23-5"></a><span class="o">}</span>
<a id="__codelineno-23-6" name="__codelineno-23-6" href="#__codelineno-23-6"></a>
<a id="__codelineno-23-7" name="__codelineno-23-7" href="#__codelineno-23-7"></a><span class="c1"># 2. Review candidates in response</span>
<a id="__codelineno-23-8" name="__codelineno-23-8" href="#__codelineno-23-8"></a>
<a id="__codelineno-23-9" name="__codelineno-23-9" href="#__codelineno-23-9"></a><span class="c1"># 3. Promote</span>
<a id="__codelineno-23-10" name="__codelineno-23-10" href="#__codelineno-23-10"></a><span class="o">{</span>
<a id="__codelineno-23-11" name="__codelineno-23-11" href="#__codelineno-23-11"></a><span class="w"> </span><span class="s2">"auto_detect"</span>:<span class="w"> </span>true,
<a id="__codelineno-23-12" name="__codelineno-23-12" href="#__codelineno-23-12"></a><span class="w"> </span><span class="s2">"dry_run"</span>:<span class="w"> </span><span class="nb">false</span>
<a id="__codelineno-23-13" name="__codelineno-23-13" href="#__codelineno-23-13"></a><span class="o">}</span>
<a id="__codelineno-23-14" name="__codelineno-23-14" href="#__codelineno-23-14"></a>
<a id="__codelineno-23-15" name="__codelineno-23-15" href="#__codelineno-23-15"></a><span class="c1"># 4. Check vault for new notes</span>
<a id="__codelineno-23-16" name="__codelineno-23-16" href="#__codelineno-23-16"></a>ls<span class="w"> </span>~/Documents/Obsidian/Vault/STM/
</code></pre></div>
<hr />
<h2 id="maintenance-tasks">Maintenance Tasks<a class="headerlink" href="#maintenance-tasks" title="Permanent link">¶</a></h2>
<h3 id="maintenance-cli">Maintenance CLI<a class="headerlink" href="#maintenance-cli" title="Permanent link">¶</a></h3>
<p>Use the built-in CLI for storage housekeeping:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-24-1" name="__codelineno-24-1" href="#__codelineno-24-1"></a><span class="c1"># Show JSONL storage stats (active counts, file sizes, compaction hints)</span>
<a id="__codelineno-24-2" name="__codelineno-24-2" href="#__codelineno-24-2"></a>cortexgraph-maintenance<span class="w"> </span>stats
<a id="__codelineno-24-3" name="__codelineno-24-3" href="#__codelineno-24-3"></a>
<a id="__codelineno-24-4" name="__codelineno-24-4" href="#__codelineno-24-4"></a><span class="c1"># Compact JSONL (rewrite files without tombstones/duplicates)</span>
<a id="__codelineno-24-5" name="__codelineno-24-5" href="#__codelineno-24-5"></a>cortexgraph-maintenance<span class="w"> </span>compact
<a id="__codelineno-24-6" name="__codelineno-24-6" href="#__codelineno-24-6"></a>
<a id="__codelineno-24-7" name="__codelineno-24-7" href="#__codelineno-24-7"></a><span class="c1"># With explicit path</span>
<a id="__codelineno-24-8" name="__codelineno-24-8" href="#__codelineno-24-8"></a>cortexgraph-maintenance<span class="w"> </span>--storage-path<span class="w"> </span>~/.config/cortexgraph/jsonl<span class="w"> </span>stats
</code></pre></div>
<h3 id="daily-maintenance-automated">Daily Maintenance (Automated)<a class="headerlink" href="#daily-maintenance-automated" title="Permanent link">¶</a></h3>
<p>Create a maintenance script <code>~/.config/cortexgraph/maintenance.sh</code>:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-25-1" name="__codelineno-25-1" href="#__codelineno-25-1"></a><span class="ch">#!/bin/bash</span>
<a id="__codelineno-25-2" name="__codelineno-25-2" href="#__codelineno-25-2"></a><span class="c1"># Mnemex Server Daily Maintenance</span>
<a id="__codelineno-25-3" name="__codelineno-25-3" href="#__codelineno-25-3"></a>
<a id="__codelineno-25-4" name="__codelineno-25-4" href="#__codelineno-25-4"></a><span class="nv">LOG_FILE</span><span class="o">=</span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.config/cortexgraph/maintenance.log"</span>
<a id="__codelineno-25-5" name="__codelineno-25-5" href="#__codelineno-25-5"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">"=== Maintenance run at </span><span class="k">$(</span>date<span class="k">)</span><span class="s2"> ==="</span><span class="w"> </span>>><span class="w"> </span><span class="s2">"</span><span class="nv">$LOG_FILE</span><span class="s2">"</span>
<a id="__codelineno-25-6" name="__codelineno-25-6" href="#__codelineno-25-6"></a>
<a id="__codelineno-25-7" name="__codelineno-25-7" href="#__codelineno-25-7"></a><span class="c1"># Backup storage</span>
<a id="__codelineno-25-8" name="__codelineno-25-8" href="#__codelineno-25-8"></a>cp<span class="w"> </span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.config/cortexgraph/jsonl/memories.jsonl"</span><span class="w"> </span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.config/cortexgraph/backups/memories.jsonl.</span><span class="k">$(</span>date<span class="w"> </span>+%Y%m%d<span class="k">)</span><span class="s2">"</span>
<a id="__codelineno-25-9" name="__codelineno-25-9" href="#__codelineno-25-9"></a>cp<span class="w"> </span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.config/cortexgraph/jsonl/relations.jsonl"</span><span class="w"> </span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.config/cortexgraph/backups/relations.jsonl.</span><span class="k">$(</span>date<span class="w"> </span>+%Y%m%d<span class="k">)</span><span class="s2">"</span>
<a id="__codelineno-25-10" name="__codelineno-25-10" href="#__codelineno-25-10"></a>
<a id="__codelineno-25-11" name="__codelineno-25-11" href="#__codelineno-25-11"></a><span class="c1"># Log stats</span>
<a id="__codelineno-25-12" name="__codelineno-25-12" href="#__codelineno-25-12"></a><span class="nb">echo</span><span class="w"> </span><span class="s2">"Storage files: </span><span class="k">$(</span>ls<span class="w"> </span>-l<span class="w"> </span><span class="nv">$HOME</span>/.config/cortexgraph/jsonl<span class="w"> </span><span class="p">|</span><span class="w"> </span>wc<span class="w"> </span>-l<span class="k">)</span><span class="s2">"</span><span class="w"> </span>>><span class="w"> </span><span class="s2">"</span><span class="nv">$LOG_FILE</span><span class="s2">"</span>
</code></pre></div>
<p>Schedule with cron:
<div class="highlight"><pre><span></span><code><a id="__codelineno-26-1" name="__codelineno-26-1" href="#__codelineno-26-1"></a><span class="c1"># Run daily at 2 AM</span>
<a id="__codelineno-26-2" name="__codelineno-26-2" href="#__codelineno-26-2"></a><span class="m">0</span><span class="w"> </span><span class="m">2</span><span class="w"> </span>*<span class="w"> </span>*<span class="w"> </span>*<span class="w"> </span>~/.config/cortexgraph/maintenance.sh
</code></pre></div></p>
<h3 id="weekly-gc">Weekly GC<a class="headerlink" href="#weekly-gc" title="Permanent link">¶</a></h3>
<p>Run garbage collection weekly:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-27-1" name="__codelineno-27-1" href="#__codelineno-27-1"></a><span class="p">{</span>
<a id="__codelineno-27-2" name="__codelineno-27-2" href="#__codelineno-27-2"></a><span class="w"> </span><span class="nt">"dry_run"</span><span class="p">:</span><span class="w"> </span><span class="kc">false</span><span class="p">,</span>
<a id="__codelineno-27-3" name="__codelineno-27-3" href="#__codelineno-27-3"></a><span class="w"> </span><span class="nt">"archive_instead"</span><span class="p">:</span><span class="w"> </span><span class="kc">true</span>
<a id="__codelineno-27-4" name="__codelineno-27-4" href="#__codelineno-27-4"></a><span class="p">}</span>
</code></pre></div>
<h3 id="monthly-review">Monthly Review<a class="headerlink" href="#monthly-review" title="Permanent link">¶</a></h3>
<ol>
<li>Check promotion candidates</li>
<li>Review archived memories</li>
<li>Adjust thresholds if needed</li>
<li>Clean up old backups</li>
</ol>
<hr />
<h2 id="monitoring">Monitoring<a class="headerlink" href="#monitoring" title="Permanent link">¶</a></h2>
<h3 id="storage-stats">Storage Stats<a class="headerlink" href="#storage-stats" title="Permanent link">¶</a></h3>
<p>Use <code>cortexgraph-search --verbose</code> or write a small script that uses <code>JSONLStorage.get_storage_stats()</code> for counts and compaction hints.</p>
<h3 id="logs">Logs<a class="headerlink" href="#logs" title="Permanent link">¶</a></h3>
<p>Server logs are written to stderr. Capture with:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-28-1" name="__codelineno-28-1" href="#__codelineno-28-1"></a>cortexgraph<span class="w"> </span><span class="m">2</span>><span class="p">&</span><span class="m">1</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>tee<span class="w"> </span>~/.config/cortexgraph/server.log
</code></pre></div>
<p>Or configure in MCP settings with log file output.</p>
<hr />
<h2 id="troubleshooting">Troubleshooting<a class="headerlink" href="#troubleshooting" title="Permanent link">¶</a></h2>
<h3 id="server-wont-start">Server won't start<a class="headerlink" href="#server-wont-start" title="Permanent link">¶</a></h3>
<ol>
<li>Check Python version: <code>python --version</code> (need 3.10+)</li>
<li>Check dependencies: <code>pip list | grep mcp</code></li>
<li>Check storage path exists: <code>ls -la ~/.config/cortexgraph/jsonl</code></li>
<li>Check permissions on storage files</li>
</ol>
<h3 id="embeddings-not-working">Embeddings not working<a class="headerlink" href="#embeddings-not-working" title="Permanent link">¶</a></h3>
<ol>
<li>Install embeddings support: <code>pip install sentence-transformers</code></li>
<li>Check model downloads: <code>~/.cache/torch/sentence_transformers/</code></li>
<li>Verify <code>CORTEXGRAPH_ENABLE_EMBEDDINGS=true</code> in config</li>
<li>Check logs for model loading errors</li>
</ol>
<h3 id="promotion-fails">Promotion fails<a class="headerlink" href="#promotion-fails" title="Permanent link">¶</a></h3>
<ol>
<li>Verify <code>BASIC_MEMORY_PATH</code> is set and valid</li>
<li>Check vault directory exists and is writable</li>
<li>Verify Obsidian vault path is correct</li>
<li>Check for file permission errors</li>
</ol>
<h3 id="storage-issues">Storage issues<a class="headerlink" href="#storage-issues" title="Permanent link">¶</a></h3>
<ol>
<li>Restore from <code>~/.config/cortexgraph/backups/memories.jsonl.*</code> and <code>relations.jsonl.*</code>.</li>
<li>To rebuild fresh storage, remove <code>~/.config/cortexgraph/jsonl</code> and restart.</li>
</ol>
<hr />
<h2 id="performance-tuning">Performance Tuning<a class="headerlink" href="#performance-tuning" title="Permanent link">¶</a></h2>
<h3 id="for-large-stores-5000-memories">For Large Stores (> 5000 memories)<a class="headerlink" href="#for-large-stores-5000-memories" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-29-1" name="__codelineno-29-1" href="#__codelineno-29-1"></a>Use<span class="w"> </span><span class="sb">`</span>JSONLStorage.compact<span class="o">()</span><span class="sb">`</span><span class="w"> </span>periodically<span class="w"> </span>to<span class="w"> </span>reclaim<span class="w"> </span>space<span class="w"> </span>from<span class="w"> </span>tombstones<span class="w"> </span>and<span class="w"> </span>duplicates.<span class="w"> </span>Consider<span class="w"> </span>a<span class="w"> </span>higher<span class="w"> </span><span class="sb">`</span>CORTEXGRAPH_FORGET_THRESHOLD<span class="sb">`</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>aggressive<span class="w"> </span>GC.
</code></pre></div>
<h3 id="for-semantic-search">For Semantic Search<a class="headerlink" href="#for-semantic-search" title="Permanent link">¶</a></h3>
<div class="highlight"><pre><span></span><code><a id="__codelineno-30-1" name="__codelineno-30-1" href="#__codelineno-30-1"></a><span class="c1"># Use lighter model</span>
<a id="__codelineno-30-2" name="__codelineno-30-2" href="#__codelineno-30-2"></a><span class="nv">CORTEXGRAPH_EMBED_MODEL</span><span class="o">=</span>all-MiniLM-L6-v2
<a id="__codelineno-30-3" name="__codelineno-30-3" href="#__codelineno-30-3"></a>
<a id="__codelineno-30-4" name="__codelineno-30-4" href="#__codelineno-30-4"></a><span class="c1"># Or faster model (less accurate)</span>
<a id="__codelineno-30-5" name="__codelineno-30-5" href="#__codelineno-30-5"></a><span class="nv">CORTEXGRAPH_EMBED_MODEL</span><span class="o">=</span>paraphrase-MiniLM-L3-v2
</code></pre></div>
<h3 id="memory-usage">Memory Usage<a class="headerlink" href="#memory-usage" title="Permanent link">¶</a></h3>
<p>Typical memory footprint:
- Base server: ~20-30MB
- With embeddings model: ~70-100MB
- Storage index in memory: ~1KB per memory (typical)</p>
<hr />
<h2 id="security-considerations">Security Considerations<a class="headerlink" href="#security-considerations" title="Permanent link">¶</a></h2>
<ol>
<li><strong>Database</strong>: Contains all short-term memories in plaintext</li>
<li>Store in user-only directory (<code>chmod 700 ~/.config/cortexgraph</code>)</li>
<li>
<p>Don't commit database to version control</p>
</li>
<li>
<p><strong>Obsidian Vault</strong>: Promoted memories written to vault</p>
</li>
<li>
<p>Consider vault encryption if storing sensitive data</p>
</li>
<li>
<p><strong>MCP Communication</strong>: Stdio transport (local only)</p>
</li>
<li>
<p>No network exposure by default</p>
</li>
<li>
<p><strong>Secrets</strong>: Don't store API keys or credentials in memories</p>
</li>
<li>Use stoplist to prevent promotion of sensitive patterns</li>
</ol>
</article>
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