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<h1 id="configuration">Configuration<a class="headerlink" href="#configuration" title="Permanent link">¶</a></h1>
<p>CortexGraph is configured via environment variables, typically stored in <code>~/.config/cortexgraph/.env</code>.</p>
<h2 id="configuration-file">Configuration File<a class="headerlink" href="#configuration-file" title="Permanent link">¶</a></h2>
<p>Create <code>~/.config/cortexgraph/.env</code>:</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"># ============================================</span>
<a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a><span class="c1"># Storage Configuration</span>
<a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>
<a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a><span class="c1"># Where short-term memories are stored (JSONL format)</span>
<a id="__codelineno-0-6" name="__codelineno-0-6" href="#__codelineno-0-6"></a><span class="nv">CORTEXGRAPH_STORAGE_PATH</span><span class="o">=</span>~/.config/cortexgraph/jsonl
<a id="__codelineno-0-7" name="__codelineno-0-7" href="#__codelineno-0-7"></a>
<a id="__codelineno-0-8" name="__codelineno-0-8" href="#__codelineno-0-8"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-9" name="__codelineno-0-9" href="#__codelineno-0-9"></a><span class="c1"># Decay Model Configuration</span>
<a id="__codelineno-0-10" name="__codelineno-0-10" href="#__codelineno-0-10"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-11" name="__codelineno-0-11" href="#__codelineno-0-11"></a>
<a id="__codelineno-0-12" name="__codelineno-0-12" href="#__codelineno-0-12"></a><span class="c1"># Decay model: power_law | exponential | two_component</span>
<a id="__codelineno-0-13" name="__codelineno-0-13" href="#__codelineno-0-13"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>power_law
<a id="__codelineno-0-14" name="__codelineno-0-14" href="#__codelineno-0-14"></a>
<a id="__codelineno-0-15" name="__codelineno-0-15" href="#__codelineno-0-15"></a><span class="c1"># Power-law model parameters</span>
<a id="__codelineno-0-16" name="__codelineno-0-16" href="#__codelineno-0-16"></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"># Power exponent (higher = faster decay)</span>
<a id="__codelineno-0-17" name="__codelineno-0-17" href="#__codelineno-0-17"></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"># Half-life in days</span>
<a id="__codelineno-0-18" name="__codelineno-0-18" href="#__codelineno-0-18"></a>
<a id="__codelineno-0-19" name="__codelineno-0-19" href="#__codelineno-0-19"></a><span class="c1"># Exponential model parameters (if CORTEXGRAPH_DECAY_MODEL=exponential)</span>
<a id="__codelineno-0-20" name="__codelineno-0-20" href="#__codelineno-0-20"></a><span class="c1"># CORTEXGRAPH_DECAY_LAMBDA=2.673e-6 # Decay constant</span>
<a id="__codelineno-0-21" name="__codelineno-0-21" href="#__codelineno-0-21"></a>
<a id="__codelineno-0-22" name="__codelineno-0-22" href="#__codelineno-0-22"></a><span class="c1"># Two-component model parameters (if CORTEXGRAPH_DECAY_MODEL=two_component)</span>
<a id="__codelineno-0-23" name="__codelineno-0-23" href="#__codelineno-0-23"></a><span class="c1"># CORTEXGRAPH_TC_LAMBDA_FAST=1.603e-5 # Fast decay constant</span>
<a id="__codelineno-0-24" name="__codelineno-0-24" href="#__codelineno-0-24"></a><span class="c1"># CORTEXGRAPH_TC_LAMBDA_SLOW=1.147e-6 # Slow decay constant</span>
<a id="__codelineno-0-25" name="__codelineno-0-25" href="#__codelineno-0-25"></a><span class="c1"># CORTEXGRAPH_TC_WEIGHT_FAST=0.7 # Weight for fast component</span>
<a id="__codelineno-0-26" name="__codelineno-0-26" href="#__codelineno-0-26"></a>
<a id="__codelineno-0-27" name="__codelineno-0-27" href="#__codelineno-0-27"></a><span class="c1"># Use count exponent (affects reinforcement)</span>
<a id="__codelineno-0-28" name="__codelineno-0-28" href="#__codelineno-0-28"></a><span class="nv">CORTEXGRAPH_DECAY_BETA</span><span class="o">=</span><span class="m">0</span>.6
<a id="__codelineno-0-29" name="__codelineno-0-29" href="#__codelineno-0-29"></a>
<a id="__codelineno-0-30" name="__codelineno-0-30" href="#__codelineno-0-30"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-31" name="__codelineno-0-31" href="#__codelineno-0-31"></a><span class="c1"># Thresholds</span>
<a id="__codelineno-0-32" name="__codelineno-0-32" href="#__codelineno-0-32"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-33" name="__codelineno-0-33" href="#__codelineno-0-33"></a>
<a id="__codelineno-0-34" name="__codelineno-0-34" href="#__codelineno-0-34"></a><span class="c1"># Forget threshold: delete memories with score < this</span>
<a id="__codelineno-0-35" name="__codelineno-0-35" href="#__codelineno-0-35"></a><span class="nv">CORTEXGRAPH_FORGET_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.05
<a id="__codelineno-0-36" name="__codelineno-0-36" href="#__codelineno-0-36"></a>
<a id="__codelineno-0-37" name="__codelineno-0-37" href="#__codelineno-0-37"></a><span class="c1"># Promote threshold: move to LTM if score >= this</span>
<a id="__codelineno-0-38" name="__codelineno-0-38" href="#__codelineno-0-38"></a><span class="nv">CORTEXGRAPH_PROMOTE_THRESHOLD</span><span class="o">=</span><span class="m">0</span>.65
<a id="__codelineno-0-39" name="__codelineno-0-39" href="#__codelineno-0-39"></a>
<a id="__codelineno-0-40" name="__codelineno-0-40" href="#__codelineno-0-40"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-41" name="__codelineno-0-41" href="#__codelineno-0-41"></a><span class="c1"># Long-Term Memory (LTM)</span>
<a id="__codelineno-0-42" name="__codelineno-0-42" href="#__codelineno-0-42"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-43" name="__codelineno-0-43" href="#__codelineno-0-43"></a>
<a id="__codelineno-0-44" name="__codelineno-0-44" href="#__codelineno-0-44"></a><span class="c1"># Obsidian vault path (for permanent storage)</span>
<a id="__codelineno-0-45" name="__codelineno-0-45" href="#__codelineno-0-45"></a><span class="nv">LTM_VAULT_PATH</span><span class="o">=</span>~/Documents/Obsidian/Vault
<a id="__codelineno-0-46" name="__codelineno-0-46" href="#__codelineno-0-46"></a>
<a id="__codelineno-0-47" name="__codelineno-0-47" href="#__codelineno-0-47"></a><span class="c1"># LTM index path (for fast search)</span>
<a id="__codelineno-0-48" name="__codelineno-0-48" href="#__codelineno-0-48"></a><span class="nv">LTM_INDEX_PATH</span><span class="o">=</span>~/.config/cortexgraph/ltm_index.jsonl
<a id="__codelineno-0-49" name="__codelineno-0-49" href="#__codelineno-0-49"></a>
<a id="__codelineno-0-50" name="__codelineno-0-50" href="#__codelineno-0-50"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-51" name="__codelineno-0-51" href="#__codelineno-0-51"></a><span class="c1"># Git Backups</span>
<a id="__codelineno-0-52" name="__codelineno-0-52" href="#__codelineno-0-52"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-53" name="__codelineno-0-53" href="#__codelineno-0-53"></a>
<a id="__codelineno-0-54" name="__codelineno-0-54" href="#__codelineno-0-54"></a><span class="c1"># Auto-commit changes to git</span>
<a id="__codelineno-0-55" name="__codelineno-0-55" href="#__codelineno-0-55"></a><span class="nv">GIT_AUTO_COMMIT</span><span class="o">=</span><span class="nb">true</span>
<a id="__codelineno-0-56" name="__codelineno-0-56" href="#__codelineno-0-56"></a>
<a id="__codelineno-0-57" name="__codelineno-0-57" href="#__codelineno-0-57"></a><span class="c1"># Commit interval in seconds (3600 = 1 hour)</span>
<a id="__codelineno-0-58" name="__codelineno-0-58" href="#__codelineno-0-58"></a><span class="nv">GIT_COMMIT_INTERVAL</span><span class="o">=</span><span class="m">3600</span>
<a id="__codelineno-0-59" name="__codelineno-0-59" href="#__codelineno-0-59"></a>
<a id="__codelineno-0-60" name="__codelineno-0-60" href="#__codelineno-0-60"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-61" name="__codelineno-0-61" href="#__codelineno-0-61"></a><span class="c1"># Embeddings (Optional)</span>
<a id="__codelineno-0-62" name="__codelineno-0-62" href="#__codelineno-0-62"></a><span class="c1"># ============================================</span>
<a id="__codelineno-0-63" name="__codelineno-0-63" href="#__codelineno-0-63"></a>
<a id="__codelineno-0-64" name="__codelineno-0-64" href="#__codelineno-0-64"></a><span class="c1"># Enable semantic search with embeddings</span>
<a id="__codelineno-0-65" name="__codelineno-0-65" href="#__codelineno-0-65"></a><span class="nv">CORTEXGRAPH_ENABLE_EMBEDDINGS</span><span class="o">=</span><span class="nb">false</span>
<a id="__codelineno-0-66" name="__codelineno-0-66" href="#__codelineno-0-66"></a>
<a id="__codelineno-0-67" name="__codelineno-0-67" href="#__codelineno-0-67"></a><span class="c1"># Embedding model (if enabled)</span>
<a id="__codelineno-0-68" name="__codelineno-0-68" href="#__codelineno-0-68"></a><span class="nv">CORTEXGRAPH_EMBED_MODEL</span><span class="o">=</span>all-MiniLM-L6-v2
</code></pre></div>
<h2 id="configuration-options">Configuration Options<a class="headerlink" href="#configuration-options" title="Permanent link">¶</a></h2>
<h3 id="decay-models">Decay Models<a class="headerlink" href="#decay-models" title="Permanent link">¶</a></h3>
<h4 id="power-law-recommended">Power-Law (Recommended)<a class="headerlink" href="#power-law-recommended" title="Permanent link">¶</a></h4>
<p>Most realistic model matching human memory:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>power_law
<a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a><span class="nv">CORTEXGRAPH_PL_ALPHA</span><span class="o">=</span><span class="m">1</span>.1
<a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a><span class="nv">CORTEXGRAPH_PL_HALFLIFE_DAYS</span><span class="o">=</span><span class="m">3</span>.0
</code></pre></div>
<ul>
<li><code>CORTEXGRAPH_PL_ALPHA</code>: Power exponent (1.0-2.0, higher = faster decay)</li>
<li><code>CORTEXGRAPH_PL_HALFLIFE_DAYS</code>: Half-life in days</li>
</ul>
<h4 id="exponential">Exponential<a class="headerlink" href="#exponential" title="Permanent link">¶</a></h4>
<p>Traditional time-based decay:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>exponential
<a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></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"># ln(2) / (3 days in seconds)</span>
</code></pre></div>
<h4 id="two-component">Two-Component<a class="headerlink" href="#two-component" title="Permanent link">¶</a></h4>
<p>Combines fast and slow decay:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a><span class="nv">CORTEXGRAPH_DECAY_MODEL</span><span class="o">=</span>two_component
<a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a><span class="nv">CORTEXGRAPH_TC_LAMBDA_FAST</span><span class="o">=</span><span class="m">1</span>.603e-5
<a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a><span class="nv">CORTEXGRAPH_TC_LAMBDA_SLOW</span><span class="o">=</span><span class="m">1</span>.147e-6
<a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a><span class="nv">CORTEXGRAPH_TC_WEIGHT_FAST</span><span class="o">=</span><span class="m">0</span>.7
</code></pre></div>
<h3 id="thresholds">Thresholds<a class="headerlink" href="#thresholds" title="Permanent link">¶</a></h3>
<p>Control memory lifecycle:</p>
<ul>
<li><strong>Forget Threshold</strong> (<code>CORTEXGRAPH_FORGET_THRESHOLD</code>): Delete if score < this</li>
<li><strong>Promote Threshold</strong> (<code>CORTEXGRAPH_PROMOTE_THRESHOLD</code>): Move to LTM if score >= this</li>
</ul>
<p>Default values (0.05, 0.65) work well for most use cases.</p>
<h3 id="storage-paths">Storage Paths<a class="headerlink" href="#storage-paths" title="Permanent link">¶</a></h3>
<ul>
<li><strong>STM</strong>: <code>CORTEXGRAPH_STORAGE_PATH</code> - JSONL files for short-term memory</li>
<li><strong>LTM</strong>: <code>LTM_VAULT_PATH</code> - Markdown files in Obsidian vault</li>
<li><strong>Index</strong>: <code>LTM_INDEX_PATH</code> - Fast search index for LTM</li>
</ul>
<h3 id="embeddings">Embeddings<a class="headerlink" href="#embeddings" title="Permanent link">¶</a></h3>
<p>Enable semantic similarity search:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a><span class="nv">CORTEXGRAPH_ENABLE_EMBEDDINGS</span><span class="o">=</span><span class="nb">true</span>
<a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a><span class="nv">CORTEXGRAPH_EMBED_MODEL</span><span class="o">=</span>all-MiniLM-L6-v2
</code></pre></div>
<p>Requires additional dependencies:
<div class="highlight"><pre><span></span><code><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>uv<span class="w"> </span>pip<span class="w"> </span>install<span class="w"> </span>sentence-transformers
</code></pre></div></p>
<h2 id="mcp-server-configuration">MCP Server Configuration<a class="headerlink" href="#mcp-server-configuration" title="Permanent link">¶</a></h2>
<h3 id="claude-desktop">Claude Desktop<a class="headerlink" href="#claude-desktop" title="Permanent link">¶</a></h3>
<p>Add to <code>~/Library/Application Support/Claude/claude_desktop_config.json</code> (macOS):</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">"cortexgraph"</span>
<a id="__codelineno-6-5" name="__codelineno-6-5" href="#__codelineno-6-5"></a><span class="w"> </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="p">}</span>
<a id="__codelineno-6-7" name="__codelineno-6-7" href="#__codelineno-6-7"></a><span class="p">}</span>
</code></pre></div>
<p>On Windows: <code>%APPDATA%\Claude\claude_desktop_config.json</code></p>
<p>On Linux: <code>~/.config/Claude/claude_desktop_config.json</code></p>
<h3 id="development-mode">Development Mode<a class="headerlink" href="#development-mode" title="Permanent link">¶</a></h3>
<p>For development/testing:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-7-1" name="__codelineno-7-1" href="#__codelineno-7-1"></a><span class="p">{</span>
<a id="__codelineno-7-2" name="__codelineno-7-2" href="#__codelineno-7-2"></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-7-3" name="__codelineno-7-3" href="#__codelineno-7-3"></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-7-4" name="__codelineno-7-4" href="#__codelineno-7-4"></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-7-5" name="__codelineno-7-5" href="#__codelineno-7-5"></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">"/absolute/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-7-6" name="__codelineno-7-6" href="#__codelineno-7-6"></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">"/absolute/path/to/cortexgraph/src"</span><span class="p">}</span>
<a id="__codelineno-7-7" name="__codelineno-7-7" href="#__codelineno-7-7"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-7-8" name="__codelineno-7-8" href="#__codelineno-7-8"></a><span class="w"> </span><span class="p">}</span>
<a id="__codelineno-7-9" name="__codelineno-7-9" href="#__codelineno-7-9"></a><span class="p">}</span>
</code></pre></div>
<h2 id="verification">Verification<a class="headerlink" href="#verification" title="Permanent link">¶</a></h2>
<p>Check configuration:</p>
<div class="highlight"><pre><span></span><code><a id="__codelineno-8-1" name="__codelineno-8-1" href="#__codelineno-8-1"></a><span class="c1"># View current config</span>
<a id="__codelineno-8-2" name="__codelineno-8-2" href="#__codelineno-8-2"></a>cat<span class="w"> </span>~/.config/cortexgraph/.env
<a id="__codelineno-8-3" name="__codelineno-8-3" href="#__codelineno-8-3"></a>
<a id="__codelineno-8-4" name="__codelineno-8-4" href="#__codelineno-8-4"></a><span class="c1"># Test MCP server</span>
<a id="__codelineno-8-5" name="__codelineno-8-5" href="#__codelineno-8-5"></a>cortexgraph
<a id="__codelineno-8-6" name="__codelineno-8-6" href="#__codelineno-8-6"></a>
<a id="__codelineno-8-7" name="__codelineno-8-7" href="#__codelineno-8-7"></a><span class="c1"># Check storage</span>
<a id="__codelineno-8-8" name="__codelineno-8-8" href="#__codelineno-8-8"></a>ls<span class="w"> </span>-la<span class="w"> </span>~/.config/cortexgraph/jsonl/
</code></pre></div>
<h2 id="next-steps">Next Steps<a class="headerlink" href="#next-steps" title="Permanent link">¶</a></h2>
<ul>
<li><a href="../quickstart/">Quick Start</a> - Start using CortexGraph with Claude</li>
<li><a href="../api/">API Reference</a> - Learn about available tools</li>
</ul>
</article>
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