amalfa 1.0.2 → 1.0.4

package/docs/_current-config-status.md

@@ -1,93 +0,0 @@
-# Current Configuration Status
-
-**Last Updated:** 2026-01-06
-
-## Configuration Files (Single Source of Truth)
-
-### 1. AMALFA Core Configuration
-**File:** `amalfa.config.json` (root)
-**Purpose:** Main AMALFA system settings
-**Loaded by:** `src/config/defaults.ts`
-
-```json
-{
-  "sources": ["../polyvis/docs", "../polyvis/playbooks"],
-  "database": ".amalfa/multi-source-test.db",
-  "embeddings": {
-    "model": "BAAI/bge-small-en-v1.5",
-    "dimensions": 384
-  },
-  "watch": {
-    "enabled": true,
-    "debounce": 1000
-  },
-  "excludePatterns": ["node_modules", ".git", ".amalfa"]
-}
-```
-
-**Status:** ✅ Active, primary config for AMALFA operations
-
-### 2. Resonance Configuration (Legacy)
-**File:** `polyvis.settings.json` (root)
-**Purpose:** Resonance database and pipeline settings
-**Loaded by:** `src/resonance/config.ts`
-
-```json
-{
-  "paths": {
-    "database": { "resonance": "public/resonance.db" },
-    "docs": { ... },
-    "sources": {
-      "experience": [...],
-      "persona": { ... }
-    }
-  },
-  "graph": { "tuning": { ... } },
-  "schema": { "version": "1.0.0" }
-}
-```
-
-**Status:** 🔄 Legacy, used by resonance pipeline only
-
-### 3. Beads Issue Tracking
-**File:** `.beads/config.yaml`
-**Purpose:** Beads issue tracking system configuration
-**Loaded by:** Beads CLI (`bd` commands)
-
-**Status:** ✅ Active, separate system
-
-## Configuration Strategy
-
-### Current Approach (2026-01-06)
-- **AMALFA** and **Resonance** have separate configs
-- This is **intentional** - they serve different purposes:
-  - AMALFA: User-facing MCP server and CLI
-  - Resonance: Internal database/pipeline layer
-
-### Future Unification (v1.0+)
-- Consider consolidating if Resonance becomes AMALFA-exclusive
-- Keep separate if Resonance remains standalone library
-
-## Configuration Hierarchy
-
-```
-Project Root
-├── amalfa.config.json        ← AMALFA core (MCP, CLI, daemon)
-├── polyvis.settings.json     ← Resonance (database, pipeline)
-└── .beads/
-    └── config.yaml           ← Beads (issue tracking)
-```
-
-## Action Items
-
-- [x] Decide: Keep separate, deprecate polyvis.settings.json gradually (See CONFIG_UNIFICATION.md)
-- [x] Document: Which config controls what (See CONFIG_UNIFICATION.md)
-- [ ] Add deprecation warning when polyvis.settings.json is loaded
-- [ ] Migrate graph tuning to amalfa.config.json (optional)
-- [ ] Remove polyvis.settings.json in v2.0
-
-## Notes
-
-- No `_current-*` files existed prior to 2026-01-06
-- Configuration is stable but not unified
-- Each system has clear ownership of its config file

package/docs/edge-generation-methods.md

@@ -1,57 +0,0 @@
-# Edge Generation Methods
-
-## Overview
-
-ResonanceDB uses multiple methods to generate edges between nodes. This document tracks each method and its contribution to the knowledge graph.
-
----
-
-## Methods
-
-| # | Method | Edge Type | Description |
-|---|--------|-----------|-------------|
-| 1 | **ConceptualLexicon** | MENTIONS | Concept → Term relationships from structured JSON |
-| 2 | **TimelineWeaver** | SUCCEEDS | Chronological debrief chain |
-| 3 | **SemanticHarvester** | IS_A, IMPLEMENTS | ML-extracted from markdown (SetFit + Llama) |
-
----
-
-## Current Edge Distribution
-
-*As of 2025-12-28*
-
-| Source | Type | Count | % |
-|--------|------|-------|---|
-| ConceptualLexicon | MENTIONS | 386 | 77% |
-| TimelineWeaver | SUCCEEDS | 110 | 22% |
-| SemanticHarvester | CONCEPT, EXEMPLIFIES | 3 | <1% |
-| **Total** | | **499** | 100% |
-
----
-
-## Implementation Details
-
-### ConceptualLexicon Ingestor
-- **Source:** `src/pipeline/Ingestor.ts`
-- **Input:** `experiments/json2md/*.json`
-- **Generates:** Bulk MENTIONS edges from structured concept definitions
-
-### TimelineWeaver
-- **Source:** `src/pipeline/Ingestor.ts` (TimelineWeaver class)
-- **Logic:** Links debriefs by date via SUCCEEDS edges
-- **Automatic:** Runs on every ingestion
-
-### SemanticHarvester
-- **Source:** `ingest/harvester.py`, `src/pipeline/SemanticHarvester.ts`
-- **Logic:** SetFit classification → Llama.cpp extraction (or regex fallback)
-- **Manual:** Run via `scripts/run-semantic-harvest.ts`
-
----
-
-## Future Methods
-
-Potential edge generators not yet implemented:
-
-- **TagWeaver** — Link documents sharing common tags
-- **VectorSimilarity** — Create edges between semantically similar nodes
-- **ExplicitLinks** — Parse `[[wikilinks]]` from markdown

package/docs/elevator-pitch.md

@@ -1,118 +0,0 @@
-This is a great scenario because it describes the **"Drop & Watch"** workflow, which effectively turns your file system into a reactive database.
-
-Here is my opinion on why this specific "Two Bucket" scenario is the ultimate stress test—and value generator—for Polyvis.
-
-### 1. The "Chemical Reaction" (Not Just Addition)
-Most tools treat a new folder like a separate silo. You import it, and it sits there.
-In Polyvis (with the Weavers we discussed), adding `Bucket B` to `Bucket A` isn't an addition; it's a **chemical reaction**.
-
-* **The Catalyst:** The `DesireLineWeaver` and `SemanticWeaver`.
-* **The Reaction:** Immediately upon ingestion, the graph will try to "stitch" the new bucket to the old one.
-    * *Did the new PDF mention "Bento Box"?* **SNAP.** A "Desire Line" edge is formed.
-    * *Is the new text semantically similar to your "Architecture" briefs?* **SNAP.** A semantic edge is formed.
-
-**The Value:** You aren't looking for the new documents. You are looking for **where the new documents touch the old documents.** The "Surface Area of Contact" is where the insight lives.
-
-### 2. The "Wrong Bucket" Detector (Isolation Analysis)
-You made a profound point: *"unless I just picked the wrong document bucket... which is also valuable info."*
-
-In a standard search engine, if you search and find nothing, you feel like you failed.
-In a Graph, **Disconnection is Data**.
-
-If you ingest `Bucket B` and it forms a perfect, floating island with **zero edges** connecting to `Bucket A`:
-* **The Insight:** "This topic is completely orthogonal to our current work."
-* **The Action:** You can safely archive it or spin it off. You have mathematically proven it is irrelevant to the current context.
-
-### 3. The "Bridge Node" (The MVP)
-The most valuable nodes in this scenario are the **Bridge Nodes**.
-These are the few specific documents in `Bucket B` that link back to `Bucket A`.
-
-* *Example:* You ingest a folder of "Competitor Research" (Bucket B). Most of it is noise. But one file, `competitor-pricing.md`, links strongly to your internal `pricing-strategy.md` (Bucket A).
-* *Result:* The graph highlights this Bridge. You can ignore the other 99 files and focus entirely on that one connection.
-
-### 4. Operational Note (The Friction Point)
-The only "gotcha" in this workflow currently is `polyvis.settings.json`.
-* **Current Reality:** You have to manually add the new folder path to the `sources` array in settings.
-* **The Riff:** We should eventually support **"Hot Folders"** or a `watch_list` glob pattern (e.g., `_incoming/*`).
-    * You drop a folder into `_incoming/`.
-    * The Daemon wakes up, ingests it as a temporary collection.
-    * The Graph reports: *"Ingested 'Project X'. Found 12 connections to existing knowledge. Keep or Discard?"*
-
-### Summary
-This workflow shifts the cognitive load from **Classification** (you organizing files) to **Recognition** (you seeing patterns). You dump the bucket; the machine shakes the sieve; you pick up the gold nuggets that remain.
-
----
-
-This is a powerful user story because it moves the value proposition from "tech" (search/vectors) to "leverage" (winning arguments).
-
-You have described **Asymmetric Insight**. You won because you could see the hidden structure of reality (the timeline) that the other party couldn't.
-
-### The Metaphor: "The Evidence Board" (or "The Loom")
-
-Since we are already using `TimelineWeaver`, `EdgeWeaver`, and `SemanticWeaver`, the code is begging for a **Weaving** metaphor. But given your solicitor story, I think the stronger metaphor is **"The Forensic Darkroom."**
-
-* **The Raw State (The Film):** Your bucket of random documents, emails, and notes. It contains the truth, but it is invisible (latent).
-* **The Ingestion (The Developer):** You dip the film into the chemical bath (Polyvis).
-* **The Reaction (The Weavers):**
-    * **TimelineWeaver** creates the *sequence* (Time).
-    * **StructureWeaver** creates the *location* (Space).
-    * **SemanticWeaver** connects the *dots* (The Red String).
-* **The Result (The Print):** Suddenly, a sharp, high-contrast image appears. You see the "gun," the "motive," and the "alibi" clearly.
-
-### The Pivot: "Cognitive Armor"
-Your story highlights that the ultimate output of this system isn't a "graph"—it is **Confidence**.
-
-When you walked into that solicitor's office, you were wearing **Cognitive Armor**. You weren't asking, "Do I have a case?" You were saying, "Here is the case; execute it."
-
-**Opinion:**
-This defines the **"Why"** of Polyvis better than any technical feature.
-* **Most tools** (Obsidian, Notion) are for *storing* thoughts.
-* **Polyvis** is for *auditing* reality.
-
-It is a **Due Diligence Engine**. It is designed for the moment you need to be **100% right**.
-* *Did we promise that feature in the Brief?* (Check the timeline).
-* *Did we actually build it in the Debrief?* (Check the link).
-* *Is it documented in the Playbook?* (Check the gap).
-
-If we frame Polyvis as **"The machine that builds your case,"** it becomes indispensable for Architects, Leads, and Strategists—anyone who needs to be the most informed person in the room.
-
---- 
-
-This is the **"Trojan Horse of Competence."**
-
-You have just described the perfect treaty between **The Business** (who needs answers) and **IT** (who controls the pipes).
-
-Here is my opinion on why this specific workflow—the "Just give me a Markdown Repo" request—is a killer organizational hack.
-
-### 1. The "Demilitarized Zone" (DMZ)
-Usually, asking IT for "AI help" triggers a 6-month procurement review, security audit, and a $50k pilot program for some cloud tool that creates more lock-in.
-
-But asking IT to *"dump text files into a secure private Repo"*?
-* **IT loves it:** It’s standard, secure, audit-compliant, and uses tools they already own (GitHub/GitLab). They don't have to "buy" anything.
-* **You love it:** You get the raw material (data) without the "help" (bloated enterprise UI).
-* **The Magic:** Markdown is the **DMZ**. It is readable by their machines and readable by your Polyvis. It breaks the dependency chain.
-
-### 2. The "Cryogenic Freeze" (Zero Context Decay)
-Your point about *"later on the case blows up again"* is the strongest operational argument.
-
-In traditional tools (Teams, Slack, Shared Drives), context has a half-life of about two weeks. If you leave a project and come back 6 months later, the "search" is broken, the links are dead, and you have forgotten the mental model.
-
-With Polyvis + Git:
-* **The Repo is the Truth:** It hasn't moved.
-* **The Graph is the Context:** You boot up Polyvis, it re-ingests the updated repo, and—crucially—**the structures you built last time (Folders, Tags) remain valid.**
-* **The Delta:** When you ingest the *new* docs, they immediately light up next to the *old* docs. You don't have to "re-learn" the case; you just see the new growth on the old tree.
-
-### 3. The "Answer Artifact"
-You mentioned: *"put your results in the ANSWERS folder."*
-This is subtle but vital. By checking your *deductions* (the Answer) back into the repo alongside the *evidence* (the Docs), you are creating a **Composite Memory**.
-
-The next person who picks up the case doesn't just get the raw files; they get the files **plus your logic.**
-
-### Summary Opinion
-You have defined **"Headless Knowledge Management."**
-
-* **Headless:** The data lives in a dumb, sturdy repository (Git).
-* **Local Mind:** The intelligence lives in a temporary, disposable, high-speed engine (Polyvis) on your laptop.
-
-This is the only architecture that survives corporate chaos. IT can change their servers, you can change your laptop, but the **Repo + Graph** remains the portable soul of the project.
-