Sharpen semantic vs grep tool descriptions, sync skill copies

- Tool docstrings: semantic_search is "the default discovery tool" that
  finds code by meaning; grep_search finds code containing exact text.
  Both have clear "when to use" / "when to use the other" sections.
- Sync codealive-context-engine skill from codealive-skills source of
  truth: add missing scripts (fetch.py, grep.py, relationships.py),
  remove deprecated explore.py, update SKILL.md with search/grep
  responsibility split.
- Both codealive-context-engine/ and plugins/ copies are now identical
  to codealive-skills source of truth.

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

Author: rodion-m

codealive-context-engine/.gitignore

@@ -0,0 +1,2 @@
+__pycache__/
+*.pyc

codealive-context-engine/README.md

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+# CodeAlive Context Engine
+
+An [agent skill](https://skills.sh/) that gives your AI coding assistant semantic understanding of your entire codebase — not just the files open in front of you, but every indexed repository, dependency, and workspace in your organization.
+
+Works with Claude Code, Cursor, GitHub Copilot, Windsurf, Gemini CLI, Codex, Goose, Amp, Roo Code, and [other agents](https://skills.sh/docs) that support the SKILL.md format.
+
+**Without this skill**, your agent can only see files you explicitly open or search for with exact keywords.
+**With this skill**, your agent understands codebase architecture, traces cross-service patterns, and answers questions about code it hasn't directly read.
+
+## Quick Start
+
+### 1. Install
+
+**Via [skills.sh](https://skills.sh/)** (recommended):
+
+```bash
+npx skills add CodeAlive-AI/codealive-skills@codealive-context-engine
+```
+
+This auto-detects your agent and installs the skill to the right location.
+
+**Manual install** — copy the skill folder to your agent's skills directory:
+
+| Agent | Project scope | User scope (all projects) |
+|-------|--------------|--------------------------|
+| Claude Code | `.claude/skills/` | `~/.claude/skills/` |
+| Cursor | `.cursor/skills/` | `~/.cursor/skills/` |
+| GitHub Copilot | `.github/skills/` | `~/.copilot/skills/` |
+| Windsurf | `.windsurf/skills/` | `~/.codeium/windsurf/skills/` |
+| Gemini CLI | `.gemini/skills/` | `~/.gemini/skills/` |
+| Codex | `.codex/skills/` | `~/.codex/skills/` |
+| Goose | `.goose/skills/` | `~/.config/goose/skills/` |
+| Amp | `.agents/skills/` | `~/.config/agents/skills/` |
+| Roo Code | `.roo/skills/` | `~/.roo/skills/` |
+| OpenCode | `.opencode/skill/` | `~/.config/opencode/skill/` |
+
+### 2. Set up
+
+Run the interactive setup — it will ask for your API key, store it securely, and verify everything works:
+
+```bash
+python setup.py
+```
+
+```
+  CodeAlive Context Engine — Setup
+  ======================================
+
+  [1/3] Checking for existing API key...
+  [2/3] API key required.
+        Get yours at: https://app.codealive.ai/settings/api-keys
+
+        Paste your API key (input is hidden): ****
+        Key verified. Connected. 7 data sources available.
+  [3/3] Storing API key...
+        Saved to macOS Keychain.
+
+  --------------------------------------
+  Ready! Start your agent and ask:
+
+    "How is authentication implemented?"
+    "Show me error handling patterns"
+    "Explain the payment processing flow"
+```
+
+The setup auto-detects your OS and stores the key in the right place (macOS Keychain, Linux secret-tool, or Windows Credential Manager).
+
+### 3. Use
+
+Start your AI coding agent and ask naturally. No special commands needed:
+
+- *"How is user authentication implemented?"*
+- *"Show me error handling patterns across our microservices"*
+- *"What libraries do we use for caching?"*
+- *"Help me understand the payment processing flow"*
+- *"Find similar features to guide my rate limiting implementation"*
+
+## Prerequisites
+
+- Python 3.8+ (no third-party packages — stdlib only)
+- A [CodeAlive](https://app.codealive.ai) account with indexed repositories
+- API key from [app.codealive.ai/settings/api-keys](https://app.codealive.ai/settings/api-keys)
+
+## How It Works
+
+The skill provides your agent with four tools that it picks from automatically:
+
+| Tool | Speed | Cost | What It Does |
+|------|-------|------|--------------|
+| **List Data Sources** | Instant | Free | Shows which repositories and workspaces are indexed |
+| **Search** | Fast | Low | Finds code locations, file paths, and snippets |
+| **Chat with Codebase** | Slower | Higher | Returns synthesized answers using server-side AI |
+| **Explore** | Slower | Higher | Multi-step workflows combining search and chat |
+
+Search is the default starting point — fast and cheap. Chat with Codebase is used when the agent needs a synthesized explanation rather than raw code locations.
+
+## Alternative Setup Methods
+
+The `setup.py` script is the recommended way. If you prefer manual configuration:
+
+**Environment variable (all platforms):**
+```bash
+export CODEALIVE_API_KEY="your_key_here"
+```
+
+**macOS Keychain:**
+```bash
+security add-generic-password -a "$USER" -s "codealive-api-key" -w "YOUR_API_KEY"
+```
+
+**Linux (secret-tool):**
+```bash
+secret-tool store --label="CodeAlive API Key" service codealive-api-key
+```
+
+**Windows Credential Manager:**
+```cmd
+cmdkey /generic:codealive-api-key /user:codealive /pass:"YOUR_API_KEY"
+```
+
+**Self-hosted instance:**
+```bash
+export CODEALIVE_BASE_URL="https://your-instance.example.com"
+```
+
+**Non-interactive setup** (CI/CD, scripted environments):
+```bash
+python setup.py --key "YOUR_API_KEY"
+python setup.py --key "YOUR_API_KEY" --env   # prints env var instruction instead of storing in credential manager
+```
+
+## Troubleshooting
+
+| Error | Fix |
+|-------|-----|
+| "API key not found" | Run `python setup.py` to configure your key |
+| "Authentication failed (401)" | Key is invalid or expired. Get a new one at [app.codealive.ai/settings/api-keys](https://app.codealive.ai/settings/api-keys) |
+| "Data sources not found" | Repository name doesn't match. Run `python scripts/datasources.py` to see available names |
+| "Cannot connect" | Check network. For self-hosted instances, verify `CODEALIVE_BASE_URL` |
+| No results | Be more specific: *"error handling in API controllers"* not just *"error handling"* |
+
+## File Structure
+
+```
+codealive-context-engine/
+  setup.py                  # Interactive setup (start here)
+  SKILL.md                  # Skill definition (read by your agent)
+  README.md                 # This file
+  scripts/
+    datasources.py          # List indexed repos and workspaces
+    search.py               # Semantic code search
+    chat.py                 # AI-powered codebase Q&A
+    explore.py              # Multi-step exploration workflows
+    lib/
+      api_client.py         # API client (auth + HTTP)
+  references/
+    query-patterns.md       # Effective query writing guide
+    workflows.md            # Step-by-step workflow examples
+```
+
+## Platform Support
+
+| Platform | Credential Store | Status |
+|----------|-----------------|--------|
+| macOS | Keychain | Fully supported |
+| Linux | freedesktop Secret Service | Fully supported |
+| Windows | Credential Manager | Fully supported |
+
+All platforms also support the `CODEALIVE_API_KEY` environment variable.
+
+No third-party Python packages required.