ultimate-pi 0.13.0 → 0.13.1

package/{.pi → .agents}/skills/ccc/SKILL.md

@@ -11,16 +11,10 @@ description: "This skill should be used when code search, file/directory summary
 
 The agent owns the `ccc` lifecycle for the current project — initialization, indexing, and searching. Do not ask the user to perform these steps; handle them automatically.
 
-- **Initialization**: If `ccc search` or `ccc index` fails with an initialization error (e.g., "Not in an initialized project directory"), run `bash "$UP_PKG/.pi/scripts/harness-cocoindex-bootstrap.sh"` from the project root (or `ccc init` + `ccc index` when not in ultimate-pi harness), then retry the original command.
+- **Initialization**: If `ccc search` or `ccc index` fails with an initialization error (e.g., "Not in an initialized project directory"), run `ccc init` from the project root directory, then `ccc index` to build the index, then retry the original command.
 - **Index freshness**: Keep the index up to date by running `ccc index` (or `ccc search --refresh`) when the index may be stale — e.g., at the start of a session, or after making significant code changes (new files, refactors, renamed modules). There is no need to re-index between consecutive searches if no code was changed in between.
 - **Installation**: If `ccc` itself is not found (command not found), refer to [management.md](references/management.md) for installation instructions and inform the user.
 
-### ultimate-pi harness
-
-- **Parent / main agents:** follow ownership above (`ccc index` when stale after large edits).
-- **`harness/planning/scout-semantic`:** use **`ccc search` only** — the harness runs incremental `ccc index` before subagent spawns. Never run `ccc index`, `ccc init`, or `ccc search --refresh` in scouts.
-- **Lane contract:** graphify = callers/communities/architecture; `ccc` = implementation-by-meaning (chunks). Do not use `ccc` for “who calls X” — use `graphify explain` / `graphify path`.
-
 ## Searching the Codebase
 
 To perform a semantic search:

package/.agents/skills/ccc/references/settings.md

@@ -0,0 +1,126 @@
+# ccc Settings
+
+Configuration lives in two YAML files, both created automatically by `ccc init`.
+
+## User-Level Settings (`~/.cocoindex_code/global_settings.yml`)
+
+Shared across all projects. Controls the embedding model and extra environment variables for the daemon.
+
+```yaml
+embedding:
+  provider: sentence-transformers   # or "litellm" (default when provider is omitted)
+  model: Snowflake/snowflake-arctic-embed-xs
+  device: mps                       # optional: cpu, cuda, mps (auto-detected if omitted)
+  min_interval_ms: 300              # optional: pace LiteLLM embedding requests to reduce 429s; defaults to 5 for LiteLLM
+
+envs:                               # extra environment variables for the daemon
+  OPENAI_API_KEY: your-key          # only needed if not already in the shell environment
+```
+
+### Fields
+
+| Field | Description |
+|-------|-------------|
+| `embedding.provider` | `sentence-transformers` for local models, `litellm` (or omit) for cloud/remote models |
+| `embedding.model` | Model identifier — format depends on provider (see examples below) |
+| `embedding.device` | Optional. `cpu`, `cuda`, or `mps`. Auto-detected if omitted. Only relevant for `sentence-transformers`. |
+| `embedding.min_interval_ms` | Optional. Minimum delay between LiteLLM embedding requests in milliseconds. Defaults to `5` for LiteLLM and is ignored by `sentence-transformers`. Set explicitly to override the default. |
+| `envs` | Key-value map of environment variables injected into the daemon. Use for API keys not already in the shell environment. |
+
+### Embedding Model Examples
+
+**Local (sentence-transformers, no API key needed):**
+
+```yaml
+embedding:
+  provider: sentence-transformers
+  model: Snowflake/snowflake-arctic-embed-xs        # default, lightweight
+```
+
+```yaml
+embedding:
+  provider: sentence-transformers
+  model: nomic-ai/CodeRankEmbed                     # better code retrieval, needs GPU (~1 GB VRAM)
+```
+
+**Ollama (local):**
+
+```yaml
+embedding:
+  model: ollama/nomic-embed-text
+```
+
+**OpenAI:**
+
+```yaml
+embedding:
+  model: text-embedding-3-small
+  min_interval_ms: 300
+envs:
+  OPENAI_API_KEY: your-api-key
+```
+
+**Gemini:**
+
+```yaml
+embedding:
+  model: gemini/gemini-embedding-001
+envs:
+  GEMINI_API_KEY: your-api-key
+```
+
+**Voyage (code-optimized):**
+
+```yaml
+embedding:
+  model: voyage/voyage-code-3
+envs:
+  VOYAGE_API_KEY: your-api-key
+```
+
+For the full list of supported cloud providers and model identifiers, see [LiteLLM Embedding Models](https://docs.litellm.ai/docs/embedding/supported_embedding).
+
+### Important
+
+Switching embedding models changes vector dimensions — you must re-index after changing the model:
+
+```bash
+ccc reset && ccc index
+```
+
+## Project-Level Settings (`<project>/.cocoindex_code/settings.yml`)
+
+Per-project. Controls which files to index. Created by `ccc init` and automatically added to `.gitignore`.
+
+```yaml
+include_patterns:
+  - "**/*.py"
+  - "**/*.js"
+  - "**/*.ts"
+  # ... (sensible defaults for 28+ file types)
+
+exclude_patterns:
+  - "**/.*"              # hidden directories
+  - "**/__pycache__"
+  - "**/node_modules"
+  - "**/dist"
+  # ...
+
+language_overrides:
+  - ext: inc             # treat .inc files as PHP
+    lang: php
+```
+
+### Fields
+
+| Field | Description |
+|-------|-------------|
+| `include_patterns` | Glob patterns for files to index. Defaults cover common languages (Python, JS/TS, Rust, Go, Java, C/C++, C#, SQL, Shell, Markdown, PHP, Lua, etc.). |
+| `exclude_patterns` | Glob patterns for files/directories to skip. Defaults exclude hidden dirs, `node_modules`, `dist`, `__pycache__`, `vendor`, etc. |
+| `language_overrides` | List of `{ext, lang}` pairs to override language detection for specific file extensions. |
+
+### Editing Tips
+
+- To index additional file types, append glob patterns to `include_patterns` (e.g. `"**/*.proto"`).
+- To exclude a directory, append to `exclude_patterns` (e.g. `"**/generated"`).
+- After editing, run `ccc index` to re-index with the new settings.

package/CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project are documented in this file.
 
 ## [Unreleased]
 
+## [v0.13.1] — 2026-05-18
+
+### 🔧 Chores
+
+- Consolidate vendored `ccc` skill under `.agents/skills/ccc`; remove redundant `cocoindex-search`, `ck-search`, and duplicate Obsidian skills from the package.
+
 ## [v0.13.0] — 2026-05-18
 
 ### ✨ Features

package/THIRD_PARTY_NOTICES.md

@@ -28,4 +28,4 @@
 - **Project:** https://github.com/cocoindex-io/cocoindex-code  
 - **License:** Apache-2.0  
 - **Install:** `uv tool install 'cocoindex-code[full]'` (see `/harness-setup` §2.4)  
-- ultimate-pi vendors the upstream agent skill at [`.pi/skills/ccc/`](.pi/skills/ccc/) and bootstraps indexes via [`.pi/scripts/harness-cocoindex-bootstrap.sh`](.pi/scripts/harness-cocoindex-bootstrap.sh). Replaces deprecated `@beaconbay/ck-search`.
+- ultimate-pi vendors the upstream agent skill at [`.agents/skills/ccc/`](.agents/skills/ccc/) and bootstraps indexes via [`.pi/scripts/harness-cocoindex-bootstrap.sh`](.pi/scripts/harness-cocoindex-bootstrap.sh). Replaces deprecated `@beaconbay/ck-search`.

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "ultimate-pi",
-	"version": "0.13.0",
+	"version": "0.13.1",
 	"description": "Ultimate AI coding harness for pi.dev — extensible skills, Obsidian wiki knowledge layer, compressed context, deterministic output",
 	"keywords": [
 		"pi-package",

package/.agents/skills/ck-search/SKILL.md

@@ -1,23 +0,0 @@
----
-name: ck-search
-description: "DEPRECATED — ck-search was removed from ultimate-pi. Use cocoindex-search or /skill:ccc instead. Triggers retained for backward compatibility: ck, ck-search, semantic search."
----
-
-# ck-search (deprecated)
-
-**`ck` / `@beaconbay/ck-search` is no longer used in this harness.**
-
-Use instead:
-
-- **`/skill:cocoindex-search`** or **`/skill:ccc`** — CocoIndex Code (`ccc search`)
-- **graphify** — architecture, callers, communities (`graphify query`, `explain`, `path`)
-
-## Migration
-
-```bash
-uv tool install 'cocoindex-code[full]'
-bash "$UP_PKG/.pi/scripts/harness-cocoindex-bootstrap.sh"
-ccc search --limit 10 "your query"
-```
-
-Remove legacy index: `rm -rf .ck` (optional).

package/.agents/skills/cocoindex-search/SKILL.md

@@ -1,35 +0,0 @@
----
-name: cocoindex-search
-description: "Semantic code search using CocoIndex Code (ccc). Use when exploring codebases, finding related implementation by meaning, or replacing legacy ck-search. Triggers on: semantic code search, ccc, cocoindex, cocoindex-code, find code related to, search the codebase for implementation, /skill:ck-search."
----
-
-# cocoindex-search
-
-CocoIndex Code (`ccc`) provides offline, AST-aware semantic search over the project codebase.
-
-## Quick start
-
-```bash
-ccc search --limit 10 "harness subagent policy"
-ccc status
-```
-
-## Full reference
-
-Load the vendored skill: **`/skill:ccc`** (`.pi/skills/ccc/SKILL.md`).
-
-## Harness lanes
-
-| Question type | Tool |
-|---------------|------|
-| Callers, callees, cross-module paths | `graphify explain` / `graphify path` |
-| Implementation by meaning | `ccc search --limit N "…"` |
-| Structural patterns | `sg -p '…'` |
-
-## Setup
-
-```bash
-bash "$UP_PKG/.pi/scripts/harness-cocoindex-bootstrap.sh"
-```
-
-Indexing before harness scouts is automatic — do not run `ccc index` or `ccc search --refresh` in `scout-semantic`.

package/.agents/skills/obsidian-bases/SKILL.md

@@ -1,299 +0,0 @@
----
-name: obsidian-bases
-description: "Create and edit Obsidian Bases (.base files): Obsidian's native database layer for dynamic tables, card views, list views, filters, formulas, and summaries over vault notes. Triggers on: create a base, add a base file, obsidian bases, base view, filter notes, formula, database view, dynamic table, task tracker base, reading list base."
-allowed-tools: Read Write
----
-
-# obsidian-bases: Obsidian's Database Layer
-
-Obsidian Bases (launched 2025) turns vault notes into queryable, dynamic views. Tables, cards, lists, maps. Defined in `.base` files. No plugin required; it is a core Obsidian feature.
-
-**Authoritative reference**: If the kepano/obsidian-skills plugin is installed, prefer its canonical obsidian-bases skill. Otherwise, use the reference below. Official docs: https://help.obsidian.md/bases/syntax
-
----
-
-## Wiki Path Resolution
-
-All `wiki/` paths in this skill (in `.base` filter expressions like `file.inFolder("wiki/")`) are relative to the wiki directory inside the Obsidian vault. Obsidian Bases operate on the vault directly; the `wiki/` prefix in filter expressions reflects the folder name within the vault. If your wiki folder has a different name, adjust filter paths accordingly.
-
----
-
-## File Format
-
-`.base` files contain valid YAML. The root keys are `filters`, `formulas`, `properties`, `summaries`, and `views`.
-
-```yaml
-# Global filters: apply to ALL views
-filters:
-  and:
-    - file.hasTag("wiki")
-    - 'status != "archived"'
-
-# Computed properties
-formulas:
-  age_days: '(now() - file.ctime).days.round(0)'
-  status_icon: 'if(status == "mature", "✅", "🔄")'
-
-# Display name overrides for properties panel
-properties:
-  status:
-    displayName: "Status"
-  formula.age_days:
-    displayName: "Age (days)"
-
-# One or more views
-views:
-  - type: table
-    name: "All Pages"
-    order:
-      - file.name
-      - type
-      - status
-      - updated
-      - formula.age_days
-```
-
----
-
-## Filters
-
-Filters select which notes appear. Applied globally or per-view.
-
-```yaml
-# Single string filter
-filters: 'status == "current"'
-
-# AND: all must be true
-filters:
-  and:
-    - 'status != "archived"'
-    - file.hasTag("wiki")
-
-# OR: any can be true
-filters:
-  or:
-    - file.hasTag("concept")
-    - file.hasTag("entity")
-
-# NOT: exclude matches
-filters:
-  not:
-    - file.inFolder("wiki/meta")
-
-# Nested
-filters:
-  and:
-    - file.inFolder("wiki/")
-    - or:
-        - 'type == "concept"'
-        - 'type == "entity"'
-```
-
-### Filter operators
-
-`==` `!=` `>` `<` `>=` `<=`
-
-### Useful filter functions
-
-| Function | Example |
-|----------|---------|
-| `file.hasTag("x")` | Notes with tag `x` |
-| `file.inFolder("path/")` | Notes in folder |
-| `file.hasLink("Note")` | Notes linking to Note |
-
----
-
-## Properties
-
-Three types:
-- **Note properties**: from frontmatter: `status`, `type`, `updated`
-- **File properties**: metadata: `file.name`, `file.mtime`, `file.size`, `file.ctime`, `file.tags`, `file.folder`
-- **Formula properties**: computed: `formula.age_days`
-
----
-
-## Formulas
-
-Defined in `formulas:`. Referenced as `formula.name` in `order:` and `properties:`.
-
-```yaml
-formulas:
-  # Days since created
-  age_days: '(now() - file.ctime).days.round(0)'
-
-  # Days until a date property
-  days_until: 'if(due_date, (date(due_date) - today()).days, "")'
-
-  # Conditional label
-  status_icon: 'if(status == "mature", "✅", if(status == "developing", "🔄", "🌱"))'
-
-  # Word count estimate
-  word_est: '(file.size / 5).round(0)'
-```
-
-**Key rule**: Subtracting two dates returns a `Duration`. Not a number. Always access `.days` first:
-```yaml
-# CORRECT
-age: '(now() - file.ctime).days'
-
-# WRONG: crashes
-age: '(now() - file.ctime).round(0)'
-```
-
-**Always guard nullable properties with `if()`**:
-```yaml
-# CORRECT
-days_left: 'if(due_date, (date(due_date) - today()).days, "")'
-```
-
----
-
-## View Types
-
-### Table
-```yaml
-views:
-  - type: table
-    name: "Wiki Index"
-    limit: 100
-    order:
-      - file.name
-      - type
-      - status
-      - updated
-    groupBy:
-      property: type
-      direction: ASC
-```
-
-### Cards
-```yaml
-views:
-  - type: cards
-    name: "Gallery"
-    order:
-      - file.name
-      - tags
-      - status
-```
-
-### List
-```yaml
-views:
-  - type: list
-    name: "Quick List"
-    order:
-      - file.name
-      - status
-```
-
----
-
-## Wiki Vault Templates
-
-### Wiki content dashboard (all non-meta pages)
-
-```yaml
-filters:
-  and:
-    - file.inFolder("wiki/")
-    - not:
-        - file.inFolder("wiki/meta")
-
-formulas:
-  age: '(now() - file.ctime).days.round(0)'
-
-properties:
-  formula.age:
-    displayName: "Age (days)"
-
-views:
-  - type: table
-    name: "All Wiki Pages"
-    order:
-      - file.name
-      - type
-      - status
-      - updated
-      - formula.age
-    groupBy:
-      property: type
-      direction: ASC
-```
-
-### Entity index (people, orgs, repos)
-
-```yaml
-filters:
-  and:
-    - file.inFolder("wiki/entities/")
-    - 'file.ext == "md"'
-
-views:
-  - type: table
-    name: "Entities"
-    order:
-      - file.name
-      - entity_type
-      - status
-      - updated
-    groupBy:
-      property: entity_type
-      direction: ASC
-```
-
-### Recent ingests
-
-```yaml
-filters:
-  and:
-    - file.inFolder("wiki/sources/")
-
-views:
-  - type: table
-    name: "Sources"
-    order:
-      - file.name
-      - source_type
-      - created
-      - status
-    groupBy:
-      property: source_type
-      direction: ASC
-```
-
----
-
-## Embedding in Notes
-
-```markdown
-![[MyBase.base]]
-
-![[MyBase.base#View Name]]
-```
-
----
-
-## Where to Save
-
-Store `.base` files in `wiki/meta/` for vault dashboards:
-- `wiki/meta/dashboard.base`: main content view
-- `wiki/meta/entities.base`: entity tracker
-- `wiki/meta/sources.base`: ingestion log
-
----
-
-## YAML Quoting Rules
-
-- Formulas with double quotes → wrap in single quotes: `'if(done, "Yes", "No")'`
-- Strings with colons or special chars → wrap in double quotes: `"Status: Active"`
-- Unquoted strings with `:` break YAML parsing
-
----
-
-## What Not to Do
-
-- Do not use `from:` or `where:`: those are Dataview syntax, not Obsidian Bases
-- Do not use `sort:` at the root level: sorting is per-view via `order:` and `groupBy:`
-- Do not put `.base` files outside the vault: they only render inside Obsidian
-- Do not reference `formula.X` in `order:` without defining `X` in `formulas:`

package/.agents/skills/obsidian-markdown/SKILL.md

@@ -1,237 +0,0 @@
----
-name: obsidian-markdown
-description: "Write correct Obsidian Flavored Markdown: wikilinks, embeds, callouts, properties, tags, highlights, math, and canvas syntax. Reference this when creating or editing any wiki page. Triggers on: write obsidian note, obsidian syntax, wikilink, callout, embed, obsidian markdown, wikilink format, callout syntax, embed syntax, obsidian formatting, how to write obsidian markdown."
-allowed-tools: Read Write Edit
----
-
-# obsidian-markdown: Obsidian Flavored Markdown
-
-Reference this skill when writing any wiki page. Obsidian extends standard Markdown with wikilinks, embeds, callouts, and properties. Getting syntax wrong causes broken links, invisible callouts, or malformed frontmatter.
-
-**Cross-reference**: If the kepano/obsidian-skills plugin is installed, prefer its canonical obsidian-markdown skill for authoritative Obsidian syntax reference. Otherwise, use the reference below. See also [github.com/kepano/obsidian-skills](https://github.com/kepano/obsidian-skills).
-
----
-
-## Wiki Path Resolution
-
-This skill provides Obsidian syntax reference. It does NOT perform file operations itself. When invoked by other skills (wiki-ingest, wiki-save, etc.), those skills handle wiki path resolution via `VAULT_WIKI_PATH`.
-
----
-
-## Wikilinks
-
-Internal links use double brackets. The filename without extension.
-
-| Syntax | What it does |
-|---|---|
-| `[[Note Name]]` | Basic link |
-| `[[Note Name\|Display Text]]` | Aliased link (shows "Display Text") |
-| `[[Note Name#Heading]]` | Link to a specific heading |
-| `[[Note Name#^block-id]]` | Link to a specific block |
-
-Rules:
-- Case-sensitive on some systems. Match the exact filename.
-- No path needed: Obsidian resolves by filename uniqueness.
-- If two files have the same name, use `[[Folder/Note Name]]` to disambiguate.
-
----
-
-## Embeds
-
-Embeds use `!` before the wikilink. They display the content inline.
-
-| Syntax | What it does |
-|---|---|
-| `![[Note Name]]` | Embed a full note |
-| `![[Note Name#Heading]]` | Embed a section |
-| `![[image.png]]` | Embed an image |
-| `![[image.png\|300]]` | Embed image with width 300px |
-| `![[document.pdf]]` | Embed a PDF (Obsidian renders natively) |
-| `![[audio.mp3]]` | Embed audio |
-
----
-
-## Callouts
-
-Callouts are blockquotes with a type keyword. They render as styled alert boxes.
-
-```markdown
-> [!note]
-> Default informational callout.
-
-> [!note] Custom Title
-> Callout with a custom title.
-
-> [!note]- Collapsible (closed by default)
-> Click to expand.
-
-> [!note]+ Collapsible (open by default)
-> Click to collapse.
-```
-
-### All callout types
-
-| Type | Aliases | Use for |
-|------|---------|---------|
-| `note` |: | General notes |
-| `abstract` | `summary`, `tldr` | Summaries |
-| `info` |: | Information |
-| `todo` |: | Action items |
-| `tip` | `hint`, `important` | Tips and highlights |
-| `success` | `check`, `done` | Positive outcomes |
-| `question` | `help`, `faq` | Open questions |
-| `warning` | `caution`, `attention` | Warnings |
-| `failure` | `fail`, `missing` | Errors or failures |
-| `danger` | `error` | Critical issues |
-| `bug` |: | Known bugs |
-| `example` |: | Examples |
-| `quote` | `cite` | Quotations |
-| `contradiction` |: | Conflicting information (wiki convention) |
-
----
-
-## Properties (Frontmatter)
-
-Obsidian renders YAML frontmatter as a Properties panel. Rules:
-
-```yaml
----
-type: concept                    # plain string
-title: "Note Title"              # quoted if it contains special chars
-created: 2026-04-08              # date as YYYY-MM-DD (not ISO datetime)
-updated: 2026-04-08
-tags:
-  - tag-one                      # list items use - format
-  - tag-two
-status: developing
-related:
-  - "[[Other Note]]"             # wikilinks must be quoted in YAML
-sources:
-  - "[[source-page]]"
----
-```
-
-Rules:
-- Flat YAML only. Never nest objects.
-- Dates as `YYYY-MM-DD`, not `2026-04-08T00:00:00`.
-- Lists as `- item`, not inline `[a, b, c]`.
-- Wikilinks in YAML must be quoted: `"[[Page]]"`.
-- `tags` field: Obsidian reads this as the tag list, searchable in vault.
-
----
-
-## Tags
-
-Two valid forms:
-
-```markdown
-#tag-name             : inline tag anywhere in the body
-#parent/child-tag     : nested tag (shows hierarchy in tag pane)
-```
-
-In frontmatter:
-```yaml
-tags:
-  - research
-  - ai/obsidian
-```
-
-Do not use `#` inside frontmatter tag lists. Just the tag name.
-
----
-
-## Text Formatting
-
-Standard Markdown plus Obsidian extensions:
-
-| Syntax | Result |
-|---|---|
-| `**bold**` | Bold |
-| `*italic*` | Italic |
-| `~~strikethrough~~` | Strikethrough |
-| `==highlight==` | Highlighted text (yellow in Obsidian) |
-| `` `inline code` `` | Inline code |
-
----
-
-## Math
-
-Obsidian uses MathJax/KaTeX:
-
-Inline math:
-```markdown
-$E = mc^2$
-```
-
-Block math:
-```markdown
-$$
-\int_0^\infty e^{-x} dx = 1
-$$
-```
-
----
-
-## Code Blocks
-
-Standard fenced code blocks. Obsidian highlights all common languages:
-
-````markdown
-```python
-def hello():
-    return "world"
-```
-````
-
----
-
-## Tables
-
-Standard Markdown tables:
-
-```markdown
-| Column A | Column B | Column C |
-|----------|----------|----------|
-| Value    | Value    | Value    |
-| Value    | Value    | Value    |
-```
-
-Obsidian renders tables natively. No plugin needed.
-
----
-
-## Mermaid Diagrams
-
-Obsidian renders Mermaid natively:
-
-````markdown
-```mermaid
-graph TD
-    A[Start] --> B{Decision}
-    B -->|Yes| C[End]
-    B -->|No| D[Loop]
-    D --> A
-```
-````
-
-Supported: `graph`, `sequenceDiagram`, `gantt`, `classDiagram`, `pie`, `flowchart`.
-
----
-
-## Footnotes
-
-```markdown
-This sentence has a footnote.[^1]
-
-[^1]: The footnote text goes here.
-```
-
----
-
-## What NOT to Do
-
-- Do not use `[link text](path/to/note.md)` for internal links: use `[[Note Name]]` instead.
-- Do not use HTML inside callouts: stick to Markdown.
-- Do not use `##` inside a callout body: headings don't render inside callouts.
-- Do not write `tags: [a, b, c]` inline in frontmatter: Obsidian prefers the list format.
-- Do not write ISO datetimes in frontmatter (`2026-04-08T00:00:00Z`): use `2026-04-08`.