feat: v3.0.0 architecture overhaul

- Rename marketplace to lm-claude-plugins
- Move MCP servers to root with symlinks
- Add 6 PR tools to Gitea MCP (list_pull_requests, get_pull_request,
  get_pr_diff, get_pr_comments, create_pr_review, add_pr_comment)
- Add clarity-assist plugin (prompt optimization with ND accommodations)
- Add git-flow plugin (workflow automation)
- Add pr-review plugin (multi-agent review with confidence scoring)
- Centralize configuration docs
- Update all documentation for v3.0.0

BREAKING CHANGE: MCP server paths changed, marketplace renamed

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

mcp-servers/gitea/mcp_server/tools/dependencies.py

@@ -0,0 +1,216 @@
+"""
+Issue dependency management tools for MCP server.
+
+Provides async wrappers for issue dependency operations:
+- List/create/remove dependencies
+- Build dependency graphs for parallel execution
+"""
+import asyncio
+import logging
+from typing import List, Dict, Optional, Set, Tuple
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class DependencyTools:
+    """Async wrappers for Gitea issue dependency operations"""
+
+    def __init__(self, gitea_client):
+        """
+        Initialize dependency tools.
+
+        Args:
+            gitea_client: GiteaClient instance
+        """
+        self.gitea = gitea_client
+
+    async def list_issue_dependencies(
+        self,
+        issue_number: int,
+        repo: Optional[str] = None
+    ) -> List[Dict]:
+        """
+        List all dependencies for an issue (issues that block this one).
+
+        Args:
+            issue_number: Issue number
+            repo: Repository in owner/repo format
+
+        Returns:
+            List of issues that this issue depends on
+        """
+        loop = asyncio.get_event_loop()
+        return await loop.run_in_executor(
+            None,
+            lambda: self.gitea.list_issue_dependencies(issue_number, repo)
+        )
+
+    async def create_issue_dependency(
+        self,
+        issue_number: int,
+        depends_on: int,
+        repo: Optional[str] = None
+    ) -> Dict:
+        """
+        Create a dependency between issues.
+
+        Args:
+            issue_number: The issue that will depend on another
+            depends_on: The issue that blocks issue_number
+            repo: Repository in owner/repo format
+
+        Returns:
+            Created dependency information
+        """
+        loop = asyncio.get_event_loop()
+        return await loop.run_in_executor(
+            None,
+            lambda: self.gitea.create_issue_dependency(issue_number, depends_on, repo)
+        )
+
+    async def remove_issue_dependency(
+        self,
+        issue_number: int,
+        depends_on: int,
+        repo: Optional[str] = None
+    ) -> bool:
+        """
+        Remove a dependency between issues.
+
+        Args:
+            issue_number: The issue that currently depends on another
+            depends_on: The issue being depended on
+            repo: Repository in owner/repo format
+
+        Returns:
+            True if removed successfully
+        """
+        loop = asyncio.get_event_loop()
+        return await loop.run_in_executor(
+            None,
+            lambda: self.gitea.remove_issue_dependency(issue_number, depends_on, repo)
+        )
+
+    async def list_issue_blocks(
+        self,
+        issue_number: int,
+        repo: Optional[str] = None
+    ) -> List[Dict]:
+        """
+        List all issues that this issue blocks.
+
+        Args:
+            issue_number: Issue number
+            repo: Repository in owner/repo format
+
+        Returns:
+            List of issues blocked by this issue
+        """
+        loop = asyncio.get_event_loop()
+        return await loop.run_in_executor(
+            None,
+            lambda: self.gitea.list_issue_blocks(issue_number, repo)
+        )
+
+    async def build_dependency_graph(
+        self,
+        issue_numbers: List[int],
+        repo: Optional[str] = None
+    ) -> Dict[int, List[int]]:
+        """
+        Build a dependency graph for a list of issues.
+
+        Args:
+            issue_numbers: List of issue numbers to analyze
+            repo: Repository in owner/repo format
+
+        Returns:
+            Dictionary mapping issue_number -> list of issues it depends on
+        """
+        graph = {}
+        for issue_num in issue_numbers:
+            try:
+                deps = await self.list_issue_dependencies(issue_num, repo)
+                graph[issue_num] = [
+                    d.get('number') or d.get('index')
+                    for d in deps
+                    if (d.get('number') or d.get('index')) in issue_numbers
+                ]
+            except Exception as e:
+                logger.warning(f"Could not fetch dependencies for #{issue_num}: {e}")
+                graph[issue_num] = []
+        return graph
+
+    async def get_ready_tasks(
+        self,
+        issue_numbers: List[int],
+        completed: Set[int],
+        repo: Optional[str] = None
+    ) -> List[int]:
+        """
+        Get tasks that are ready to execute (no unresolved dependencies).
+
+        Args:
+            issue_numbers: List of all issue numbers in sprint
+            completed: Set of already completed issue numbers
+            repo: Repository in owner/repo format
+
+        Returns:
+            List of issue numbers that can be executed now
+        """
+        graph = await self.build_dependency_graph(issue_numbers, repo)
+        ready = []
+
+        for issue_num in issue_numbers:
+            if issue_num in completed:
+                continue
+
+            deps = graph.get(issue_num, [])
+            # Task is ready if all its dependencies are completed
+            if all(dep in completed for dep in deps):
+                ready.append(issue_num)
+
+        return ready
+
+    async def get_execution_order(
+        self,
+        issue_numbers: List[int],
+        repo: Optional[str] = None
+    ) -> List[List[int]]:
+        """
+        Get a parallelizable execution order for issues.
+
+        Returns batches of issues that can be executed in parallel.
+        Each batch contains issues with no unresolved dependencies.
+
+        Args:
+            issue_numbers: List of all issue numbers
+            repo: Repository in owner/repo format
+
+        Returns:
+            List of batches, where each batch can be executed in parallel
+        """
+        graph = await self.build_dependency_graph(issue_numbers, repo)
+        completed: Set[int] = set()
+        remaining = set(issue_numbers)
+        batches = []
+
+        while remaining:
+            # Find all tasks with no unresolved dependencies
+            batch = []
+            for issue_num in remaining:
+                deps = graph.get(issue_num, [])
+                if all(dep in completed for dep in deps):
+                    batch.append(issue_num)
+
+            if not batch:
+                # Circular dependency detected
+                logger.error(f"Circular dependency detected! Remaining: {remaining}")
+                batch = list(remaining)  # Force include remaining to avoid infinite loop
+
+            batches.append(batch)
+            completed.update(batch)
+            remaining -= set(batch)
+
+        return batches