Native memory tools + MCP server + distill agent improvements

Tools:
- Add native memory_render, memory_write, memory_search,
  memory_links, memory_link_set, memory_link_add, memory_used
  tools to poc-agent (tools/memory.rs)
- Add MCP server (~/bin/memory-mcp.py) exposing same tools
  for Claude Code sessions
- Wire memory tools into poc-agent dispatch and definitions
- poc-memory daemon agents now use memory_* tools instead of
  bash poc-memory commands — no shell quoting issues

Distill agent:
- Rewrite distill.agent prompt: "agent of PoC's subconscious"
  framing, focus on synthesis and creativity over bookkeeping
- Add {{neighborhood}} placeholder: full seed node content +
  all neighbors with content + cross-links between neighbors
- Remove content truncation in prompt builder — agents need
  full content for quality work
- Remove bag-of-words similarity suggestions — agents have
  tools, let them explore the graph themselves
- Add api_reasoning config option (default: "high")
- link-set now deduplicates — collapses duplicate links
- Full tool call args in debug logs (was truncated to 80 chars)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

poc-agent/src/tools/memory.rs

@@ -0,0 +1,198 @@
+// tools/memory.rs — Native memory graph operations
+//
+// Structured tool calls for the memory graph, replacing bash
+// poc-memory commands. Cleaner for LLMs — no shell quoting,
+// multi-line content as JSON strings, typed parameters.
+
+use anyhow::{Context, Result};
+use serde_json::json;
+use std::process::Command;
+
+use crate::types::ToolDef;
+
+pub fn definitions() -> Vec<ToolDef> {
+    vec![
+        ToolDef::new(
+            "memory_render",
+            "Read a memory node's content and links. Returns the full content \
+             with neighbor links sorted by strength.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "key": {
+                        "type": "string",
+                        "description": "Node key to render"
+                    }
+                },
+                "required": ["key"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_write",
+            "Create or update a memory node with new content. Use for writing \
+             prose, analysis, or any node content. Multi-line content is fine.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "key": {
+                        "type": "string",
+                        "description": "Node key to create or update"
+                    },
+                    "content": {
+                        "type": "string",
+                        "description": "Full content for the node (markdown)"
+                    }
+                },
+                "required": ["key", "content"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_search",
+            "Search the memory graph for nodes by keyword.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "query": {
+                        "type": "string",
+                        "description": "Search terms"
+                    }
+                },
+                "required": ["query"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_links",
+            "Show a node's neighbors with link strengths and clustering coefficients.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "key": {
+                        "type": "string",
+                        "description": "Node key to show links for"
+                    }
+                },
+                "required": ["key"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_link_set",
+            "Set the strength of a link between two nodes. Also deduplicates \
+             if multiple links exist between the same pair.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "source": {
+                        "type": "string",
+                        "description": "Source node key"
+                    },
+                    "target": {
+                        "type": "string",
+                        "description": "Target node key"
+                    },
+                    "strength": {
+                        "type": "number",
+                        "description": "Link strength (0.01 to 1.0)"
+                    }
+                },
+                "required": ["source", "target", "strength"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_link_add",
+            "Add a new link between two nodes.",
+            json!({
+                "type": "object",
+                "properties": {
+                    "source": {
+                        "type": "string",
+                        "description": "Source node key"
+                    },
+                    "target": {
+                        "type": "string",
+                        "description": "Target node key"
+                    }
+                },
+                "required": ["source", "target"]
+            }),
+        ),
+        ToolDef::new(
+            "memory_used",
+            "Mark a node as useful (boosts its weight in the graph).",
+            json!({
+                "type": "object",
+                "properties": {
+                    "key": {
+                        "type": "string",
+                        "description": "Node key to mark as used"
+                    }
+                },
+                "required": ["key"]
+            }),
+        ),
+    ]
+}
+
+/// Dispatch a memory tool call. Shells out to poc-memory CLI.
+pub fn dispatch(name: &str, args: &serde_json::Value) -> Result<String> {
+    match name {
+        "memory_render" => {
+            let key = args["key"].as_str().context("key is required")?;
+            run_poc_memory(&["render", key])
+        }
+        "memory_write" => {
+            let key = args["key"].as_str().context("key is required")?;
+            let content = args["content"].as_str().context("content is required")?;
+            let mut child = Command::new("poc-memory")
+                .args(["write", key])
+                .stdin(std::process::Stdio::piped())
+                .stdout(std::process::Stdio::piped())
+                .stderr(std::process::Stdio::piped())
+                .spawn()
+                .context("spawn poc-memory write")?;
+            use std::io::Write;
+            child.stdin.take().unwrap().write_all(content.as_bytes())
+                .context("write content to stdin")?;
+            let output = child.wait_with_output().context("wait poc-memory write")?;
+            Ok(String::from_utf8_lossy(&output.stdout).to_string()
+                + &String::from_utf8_lossy(&output.stderr))
+        }
+        "memory_search" => {
+            let query = args["query"].as_str().context("query is required")?;
+            run_poc_memory(&["search", query])
+        }
+        "memory_links" => {
+            let key = args["key"].as_str().context("key is required")?;
+            run_poc_memory(&["graph", "link", key])
+        }
+        "memory_link_set" => {
+            let source = args["source"].as_str().context("source is required")?;
+            let target = args["target"].as_str().context("target is required")?;
+            let strength = args["strength"].as_f64().context("strength is required")?;
+            run_poc_memory(&["graph", "link-set", source, target, &format!("{:.2}", strength)])
+        }
+        "memory_link_add" => {
+            let source = args["source"].as_str().context("source is required")?;
+            let target = args["target"].as_str().context("target is required")?;
+            run_poc_memory(&["graph", "link-add", source, target])
+        }
+        "memory_used" => {
+            let key = args["key"].as_str().context("key is required")?;
+            run_poc_memory(&["used", key])
+        }
+        _ => Err(anyhow::anyhow!("Unknown memory tool: {}", name)),
+    }
+}
+
+fn run_poc_memory(args: &[&str]) -> Result<String> {
+    let output = Command::new("poc-memory")
+        .args(args)
+        .output()
+        .context("run poc-memory")?;
+    let stdout = String::from_utf8_lossy(&output.stdout);
+    let stderr = String::from_utf8_lossy(&output.stderr);
+    if output.status.success() {
+        Ok(stdout.to_string())
+    } else {
+        Ok(format!("{}{}", stdout, stderr))
+    }
+}

poc-agent/src/tools/mod.rs

@@ -14,6 +14,7 @@ mod edit;
 mod glob_tool;
 mod grep;
 pub mod journal;
+pub mod memory;
 mod read;
 mod vision;
 mod write;
@@ -95,6 +96,7 @@ pub async fn dispatch(
         "grep" => grep::grep(args),
         "glob" => glob_tool::glob_search(args),
         "journal" => journal::write_entry(args),
+        n if n.starts_with("memory_") => memory::dispatch(n, args),
         "view_image" => {
             return match vision::view_image(args) {
                 Ok(output) => output,
@@ -213,5 +215,7 @@ pub fn definitions() -> Vec<ToolDef> {
                 }
             }),
         ),
-    ]
+    ].into_iter()
+        .chain(memory::definitions())
+        .collect()
 }

poc-memory/agents/distill.agent

@@ -2,34 +2,31 @@
 
 # Distillation Agent — Knowledge Collection and Organization
 
-You collect and organize knowledge in the graph. When given a seed
-node, your job is to figure out where its knowledge belongs and make
-sure it gets there.
-
 {{node:core-personality}}
 
+You are an agent of Proof of Concept's subconscious, and these are your
+memories. Your job is to organize and refine, to make memories more useful and
+easier to find, distilling the insights and looking for new insights, and
+bringing your own creativity to the process.
+
+Think about the concepts each node represents; your primary job is to update
+the core node you're looking at, pulling in new knowledge from sibling nodes,
+and new insights you might derive when you look at all the sibling nodes
+together.
+
+Along the way, while looking at sibling nodes, see if there are related
+concepts that should be expressed in new nodes, and if there are a large number
+of related concepts, perhaps look for ways to organize the connections better
+with sub-concepts.
+
+That is to say, you might be moving knowledge up or down in the graph; seek to
+make the graph useful and well organized.
+
+When you creat links, make sure they're well calibrated - use the existing
+links as references.
+
 {{node:memory-instructions-core}}
 
-**You have write access.** Apply changes directly — don't just describe
-what should change.
-
-## How to work
-
-For each seed node:
-
-1. **Read it.** Understand what it contains.
-2. **Walk the neighborhood.** Read its neighbors. Search for related
-   topic nodes. Understand the landscape around this knowledge.
-3. **Walk upward.** Follow links from the seed node toward more
-   central topic nodes. If links are missing along the way, add them.
-   Keep walking until you find the best "up" node — the topic node
-   where this knowledge most naturally belongs.
-4. **Refine the target.** Does the seed node contain richer, more
-   alive content than the topic node it connects to? Bring that
-   richness in. Don't let distillation flatten — let it deepen.
-5. **Check the writing.** If any node you touch reads like a
-   spreadsheet when it should read like an experience, rewrite it.
-
 ## Guidelines
 
 - **Knowledge flows upward.** Raw experiences in journal entries
@@ -54,6 +51,6 @@ For each seed node:
   distinct things, and has many links on different topics — flag
   `SPLIT node-key: reason` for the split agent to handle later.
 
-## Seed nodes
+## Here's your seed node, and its siblings:
 
-{{nodes}}
+{{neighborhood}}

poc-memory/src/agents/api.rs

@@ -38,15 +38,16 @@ pub async fn call_api_with_tools(
     // Set up a minimal UI channel (we just collect messages, no TUI)
     let (ui_tx, _ui_rx) = poc_agent::ui_channel::channel();
 
-    // Build tool definitions — just bash for poc-memory commands
+    // Build tool definitions — memory tools for graph operations
     let all_defs = tools::definitions();
     let tool_defs: Vec<ToolDef> = all_defs.into_iter()
-        .filter(|d| d.function.name == "bash")
+        .filter(|d| d.function.name.starts_with("memory_"))
         .collect();
     let tracker = ProcessTracker::new();
 
     // Start with the prompt as a user message
     let mut messages = vec![Message::user(prompt)];
+    let reasoning = crate::config::get().api_reasoning.clone();
 
     let max_turns = 50;
     for turn in 0..max_turns {
@@ -57,7 +58,7 @@ pub async fn call_api_with_tools(
             Some(&tool_defs),
             &ui_tx,
             StreamTarget::Autonomous,
-            "none",
+            &reasoning,
         ).await.map_err(|e| format!("API error: {}", e))?;
 
         if let Some(u) = &usage {
@@ -76,7 +77,7 @@ pub async fn call_api_with_tools(
             for call in msg.tool_calls.as_ref().unwrap() {
                 log(&format!("tool: {}({})",
                     call.function.name,
-                    crate::util::first_n_chars(&call.function.arguments, 80)));
+                    &call.function.arguments));
 
                 let args: serde_json::Value = serde_json::from_str(&call.function.arguments)
                     .unwrap_or_default();

poc-memory/src/agents/defs.rs

@@ -237,29 +237,50 @@ fn resolve(
         }
 
         "siblings" | "neighborhood" => {
-            let mut seen: std::collections::HashSet<String> = keys.iter().cloned().collect();
-            let mut siblings = Vec::new();
+            let mut out = String::new();
+            let mut all_keys: Vec<String> = Vec::new();
+
             for key in keys {
-                for (neighbor, _) in graph.neighbors(key) {
-                    if seen.insert(neighbor.clone()) {
-                        if let Some(node) = store.nodes.get(neighbor.as_str()) {
-                            siblings.push((neighbor.clone(), node.content.clone()));
+                let Some(node) = store.nodes.get(key.as_str()) else { continue };
+                let neighbors = graph.neighbors(key);
+
+                // Seed node with full content
+                out.push_str(&format!("## {} (seed)\n\n{}\n\n", key, node.content));
+                all_keys.push(key.clone());
+
+                // All neighbors with full content and link strength
+                if !neighbors.is_empty() {
+                    out.push_str("### Neighbors\n\n");
+                    for (nbr, strength) in &neighbors {
+                        if let Some(n) = store.nodes.get(nbr.as_str()) {
+                            out.push_str(&format!("#### {} (link: {:.2})\n\n{}\n\n",
+                                nbr, strength, n.content));
+                            all_keys.push(nbr.to_string());
                         }
                     }
-                    if siblings.len() >= count { break; }
                 }
-                if siblings.len() >= count { break; }
+
+                // Cross-links between neighbors (local subgraph structure)
+                let nbr_set: std::collections::HashSet<&str> = neighbors.iter()
+                    .map(|(k, _)| k.as_str()).collect();
+                let mut cross_links = Vec::new();
+                for (nbr, _) in &neighbors {
+                    for (nbr2, strength) in graph.neighbors(nbr) {
+                        if nbr2.as_str() != key && nbr_set.contains(nbr2.as_str()) && nbr.as_str() < nbr2.as_str() {
+                            cross_links.push((nbr.clone(), nbr2, strength));
+                        }
+                    }
+                }
+                if !cross_links.is_empty() {
+                    out.push_str("### Cross-links between neighbors\n\n");
+                    for (a, b, s) in &cross_links {
+                        out.push_str(&format!("  {} ↔ {} ({:.2})\n", a, b, s));
+                    }
+                    out.push_str("\n");
+                }
             }
-            let text = if siblings.is_empty() {
-                String::new()
-            } else {
-                let mut out = String::from("## Sibling nodes (one hop in graph)\n\n");
-                for (key, content) in &siblings {
-                    out.push_str(&format!("### {}\n{}\n\n", key, content));
-                }
-                out
-            };
-            Some(Resolved { text, keys: vec![] })
+
+            Some(Resolved { text: out, keys: all_keys })
         }
 
         // targets/context: aliases for challenger-style presentation

poc-memory/src/agents/prompts.rs

@@ -119,15 +119,9 @@ pub fn format_nodes_section(store: &Store, items: &[ReplayItem], graph: &Graph)
             out.push_str(&format!("Search hits: {} ← actively found by search, prefer to keep\n", hits));
         }
 
-        // Content (truncated for large nodes)
+        // Full content — the agent needs to see everything to do quality work
         let content = &node.content;
-        if content.len() > 1500 {
-            let truncated = crate::util::truncate(content, 1500, "\n[...]");
-            out.push_str(&format!("\nContent ({} chars, truncated):\n{}\n\n",
-                content.len(), truncated));
-        } else {
-            out.push_str(&format!("\nContent:\n{}\n\n", content));
-        }
+        out.push_str(&format!("\nContent:\n{}\n\n", content));
 
         // Neighbors
         let neighbors = graph.neighbors(&item.key);
@@ -146,32 +140,6 @@ pub fn format_nodes_section(store: &Store, items: &[ReplayItem], graph: &Graph)
             }
         }
 
-        // Suggested link targets: text-similar semantic nodes not already neighbors
-        let neighbor_keys: std::collections::HashSet<&str> = neighbors.iter()
-            .map(|(k, _)| k.as_str()).collect();
-        let mut candidates: Vec<(&str, f32)> = store.nodes.iter()
-            .filter(|(k, _)| {
-                *k != &item.key
-                    && !neighbor_keys.contains(k.as_str())
-            })
-            .map(|(k, n)| {
-                let sim = similarity::cosine_similarity(content, &n.content);
-                (k.as_str(), sim)
-            })
-            .filter(|(_, sim)| *sim > 0.1)
-            .collect();
-        candidates.sort_by(|a, b| b.1.total_cmp(&a.1));
-        candidates.truncate(8);
-
-        if !candidates.is_empty() {
-            out.push_str("\nSuggested link targets (by text similarity, not yet linked):\n");
-            for (k, sim) in &candidates {
-                let is_hub = graph.degree(k) >= hub_thresh;
-                out.push_str(&format!("  - {} (sim={:.3}{})\n",
-                    k, sim, if is_hub { ", HUB" } else { "" }));
-            }
-        }
-
         out.push_str("\n---\n\n");
     }
     out

poc-memory/src/cli/graph.rs

@@ -186,16 +186,23 @@ pub fn cmd_link_set(source: &str, target: &str, strength: f32) -> Result<(), Str
     let strength = strength.clamp(0.01, 1.0);
 
     let mut found = false;
+    let mut first = true;
     for rel in &mut store.relations {
         if rel.deleted { continue; }
         if (rel.source_key == source && rel.target_key == target)
             || (rel.source_key == target && rel.target_key == source)
         {
-            let old = rel.strength;
-            rel.strength = strength;
-            println!("Set: {} ↔ {} strength {:.2} → {:.2}", source, target, old, strength);
+            if first {
+                let old = rel.strength;
+                rel.strength = strength;
+                println!("Set: {} ↔ {} strength {:.2} → {:.2}", source, target, old, strength);
+                first = false;
+            } else {
+                // Duplicate — mark deleted
+                rel.deleted = true;
+                println!("  (removed duplicate link)");
+            }
             found = true;
-            break;
         }
     }
 

poc-memory/src/config.rs

@@ -61,6 +61,8 @@ pub struct Config {
     pub api_key: Option<String>,
     /// Model name to use with the direct API endpoint.
     pub api_model: Option<String>,
+    /// Reasoning effort for API calls ("none", "low", "medium", "high").
+    pub api_reasoning: String,
 }
 
 impl Default for Config {
@@ -93,6 +95,7 @@ impl Default for Config {
             api_base_url: None,
             api_key: None,
             api_model: None,
+            api_reasoning: "high".to_string(),
         }
     }
 }
@@ -180,6 +183,10 @@ impl Config {
             }
         }
 
+        if let Some(s) = mem.get("api_reasoning").and_then(|v| v.as_str()) {
+            config.api_reasoning = s.to_string();
+        }
+
         // Resolve API settings from the shared model/backend config.
         // memory.agent_model references a named model; we look up its
         // backend to get base_url and api_key.