feat: increase test coverage and improve CLI test suite

.github/workflows/release.yml

@@ -15,6 +15,9 @@ env:
   CARGO_TERM_COLOR: always
   RUST_BACKTRACE: 1
 
+permissions:
+  contents: write
+
 jobs:
   verify-version:
     name: Verify Version

.gitignore

@@ -322,4 +322,5 @@ commondir
 gitdir
 index
 .newton
-CLAUDE.md
+CLAUDE.md
+repomix-output.xml

.repomixignore

@@ -0,0 +1,9 @@
+# Add patterns to ignore here, one per line
+# Example:
+# *.log
+# tmp/
+*.md
+*.lcov
+webdocs
+tests
+.github

README.md

@@ -160,12 +160,34 @@ For detailed Kubernetes deployment instructions, see the [Kubernetes Deployment
 
 ### 1. Configure FastSkill
 
-Create `.fastskill.yaml` in your project root:
+Create `skill-project.toml` in your project root:
 
-```yaml
-embedding:
-  openai_base_url: "https://api.openai.com/v1"
-  embedding_model: "text-embedding-3-small"
+```toml
+[metadata]
+id = "my-project"
+version = "1.0.0"
+
+[dependencies]
+# Add skill dependencies here
+
+[tool.fastskill]
+skills_directory = ".claude/skills"
+
+[tool.fastskill.embedding]
+openai_base_url = "https://api.openai.com/v1"
+embedding_model = "text-embedding-3-small"
+
+[[tool.fastskill.repositories]]
+name = "anthropic"
+type = "git-marketplace"
+url = "https://github.com/anthropics/skills"
+priority = 0
+```
+
+Or use the init command:
+
+```bash
+fastskill init
 ```
 
 Set your OpenAI API key:
@@ -241,39 +263,66 @@ FastSkill provides a unified repository system for managing all skill storage lo
 - **ZIP URL sources** (static hosting with marketplace.json)
 - **Local folders** (for development)
 
-All repository types are configured in `.claude/repositories.toml` (or automatically loaded from `sources.toml` and `registries.toml` for backward compatibility).
+All repository types are configured in `skill-project.toml` under `[[tool.fastskill.repositories]]`.
 
 For detailed repository setup, usage, and management instructions, see [docs/REGISTRY.md](docs/REGISTRY.md).
 
 ## Configuration
 
-Create `.fastskill.yaml` in your project root:
+FastSkill uses `skill-project.toml` as the unified configuration file for both project-level and skill-level contexts.
+
+### skill-project.toml Structure
+
+```toml
+[metadata]
+id = "my-skill"
+version = "1.0.0"
 
-```yaml
-embedding:
-  openai_base_url: "https://api.openai.com/v1"
-  embedding_model: "text-embedding-3-small"
+[dependencies]
+# Add your skill dependencies here
 
-# Optional: Custom skills directory
-skills_directory: ".claude/skills"
+[tool.fastskill]
+skills_directory = ".claude/skills"
+
+[tool.fastskill.embedding]
+openai_base_url = "https://api.openai.com/v1"
+embedding_model = "text-embedding-3-small"
+
+[[tool.fastskill.repositories]]
+name = "anthropic"
+type = "git-marketplace"
+url = "https://github.com/anthropics/skills"
+priority = 0
 ```
 
-The CLI resolves the skills directory using this priority:
+### Configuration Resolution
+
+The CLI resolves configuration from `skill-project.toml`:
+
+1. Searches current directory and parents for `skill-project.toml`
+2. Extracts `[tool.fastskill]` section for skills directory and embedding config
+3. Extracts `[tool.fastskill.repositories]` for repository sources
+4. Defaults to `.claude/skills/` if no skills_directory is configured
+
+### Quick Setup
 
-1. `skills_directory` from `.fastskill.yaml`
-2. Walk up directory tree to find existing `.claude/skills/`
-3. Default to `.claude/skills/` in current directory (doesn't auto-create)
+```bash
+# Initialize a new project
+fastskill init
+
+# Set OpenAI API key for semantic search
+export OPENAI_API_KEY="your-key-here"
+```
 
 ## Troubleshooting
 
 ### Configuration Not Found
 
 If you see "Embedding configuration required but not found":
 
-1. Create `.fastskill.yaml` with embedding configuration (see Quick Start section)
-2. Set `OPENAI_API_KEY` environment variable
-
-**Note**: The error message may mention `fastskill init`, but that command is for skill authors only. For project setup, manually create `.fastskill.yaml` as shown in Quick Start.
+1. Run `fastskill init` to create `skill-project.toml`
+2. Add `[tool.fastskill.embedding]` section with embedding configuration
+3. Set `OPENAI_API_KEY` environment variable
 
 ### API Key Issues
 

coverage-after/html/control.js

@@ -0,0 +1,99 @@
+
+function next_uncovered(selector, reverse, scroll_selector) {
+  function visit_element(element) {
+    element.classList.add("seen");
+    element.classList.add("selected");
+
+    if (!scroll_selector) {
+      scroll_selector = "tr:has(.selected) td.line-number"
+    }
+
+    const scroll_to = document.querySelector(scroll_selector);
+    if (scroll_to) {
+      scroll_to.scrollIntoView({behavior: "smooth", block: "center", inline: "end"});
+    }
+  }
+
+  function select_one() {
+    if (!reverse) {
+      const previously_selected = document.querySelector(".selected");
+
+      if (previously_selected) {
+        previously_selected.classList.remove("selected");
+      }
+
+      return document.querySelector(selector + ":not(.seen)");
+    } else {
+      const previously_selected = document.querySelector(".selected");
+
+      if (previously_selected) {
+        previously_selected.classList.remove("selected");
+        previously_selected.classList.remove("seen");
+      }
+
+      const nodes = document.querySelectorAll(selector + ".seen");
+      if (nodes) {
+        const last = nodes[nodes.length - 1]; // last
+        return last;
+      } else {
+        return undefined;
+      }
+    }
+  }
+
+  function reset_all() {
+    if (!reverse) {
+      const all_seen = document.querySelectorAll(selector + ".seen");
+
+      if (all_seen) {
+        all_seen.forEach(e => e.classList.remove("seen"));
+      }
+    } else {
+      const all_seen = document.querySelectorAll(selector + ":not(.seen)");
+
+      if (all_seen) {
+        all_seen.forEach(e => e.classList.add("seen"));
+      }
+    }
+
+  }
+
+  const uncovered = select_one();
+
+  if (uncovered) {
+    visit_element(uncovered);
+  } else {
+    reset_all();
+
+    const uncovered = select_one();
+
+    if (uncovered) {
+      visit_element(uncovered);
+    }
+  }
+}
+
+function next_line(reverse) {
+  next_uncovered("td.uncovered-line", reverse)
+}
+
+function next_region(reverse) {
+  next_uncovered("span.red.region", reverse);
+}
+
+function next_branch(reverse) {
+  next_uncovered("span.red.branch", reverse);
+}
+
+document.addEventListener("keypress", function(event) {
+  const reverse = event.shiftKey;
+  if (event.code == "KeyL") {
+    next_line(reverse);
+  }
+  if (event.code == "KeyB") {
+    next_branch(reverse);
+  }
+  if (event.code == "KeyR") {
+    next_region(reverse);
+  }
+});