llm-ide-rules 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

llm_ide_rules/commands/delete.py

@@ -7,7 +7,58 @@ import typer
 from typing_extensions import Annotated
 
 from llm_ide_rules.commands.download import INSTRUCTION_TYPES, DEFAULT_TYPES
+from llm_ide_rules.constants import header_to_filename
 from llm_ide_rules.log import log
+from llm_ide_rules.markdown_parser import parse_sections
+
+
+def get_generated_files(target_dir: Path) -> set[Path]:
+    """Identify files that would be generated from local instruction files."""
+    generated = set()
+
+    # Check instructions.md
+    instructions_path = target_dir / "instructions.md"
+    if instructions_path.exists():
+        try:
+            general, sections = parse_sections(instructions_path.read_text())
+
+            # If general instructions exist, these files are generated
+            if any(line.strip() for line in general):
+                generated.add(target_dir / ".cursor/rules/general.mdc")
+                generated.add(target_dir / ".github/copilot-instructions.md")
+                generated.add(target_dir / "CLAUDE.md")
+
+            # If any sections exist, root docs are definitely generated
+            if sections:
+                generated.add(target_dir / "CLAUDE.md")
+
+            # Section specific files
+            for header in sections:
+                filename = header_to_filename(header)
+                generated.add(target_dir / f".cursor/rules/{filename}.mdc")
+                generated.add(
+                    target_dir / f".github/instructions/{filename}.instructions.md"
+                )
+
+        except Exception as e:
+            log.warning("failed to parse instructions.md", error=str(e))
+
+    # Check commands.md
+    commands_path = target_dir / "commands.md"
+    if commands_path.exists():
+        try:
+            _, sections = parse_sections(commands_path.read_text())
+            for header in sections:
+                filename = header_to_filename(header)
+                generated.add(target_dir / f".cursor/commands/{filename}.md")
+                generated.add(target_dir / f".github/prompts/{filename}.prompt.md")
+                generated.add(target_dir / f".gemini/commands/{filename}.toml")
+                generated.add(target_dir / f".claude/commands/{filename}.md")
+                generated.add(target_dir / f".opencode/commands/{filename}.md")
+        except Exception as e:
+            log.warning("failed to parse commands.md", error=str(e))
+
+    return {p.resolve() for p in generated}
 
 
 def find_files_to_delete(
@@ -38,6 +89,11 @@ def find_files_to_delete(
             if file_path.exists() and file_path.is_file():
                 files_to_delete.append(file_path)
 
+        for file_name in config.get("generated_files", []):
+            file_path = target_dir / file_name
+            if file_path.exists() and file_path.is_file():
+                files_to_delete.append(file_path)
+
         for file_pattern in config.get("recursive_files", []):
             matching_files = list(target_dir.rglob(file_pattern))
             files_to_delete.extend([f for f in matching_files if f.is_file()])
@@ -49,12 +105,19 @@ def delete_main(
     instruction_types: Annotated[
         list[str] | None,
         typer.Argument(
-            help="Types of instructions to delete (cursor, github, gemini, claude, agent, agents). Deletes everything by default."
+            help="Types of instructions to delete (cursor, github, gemini, claude, opencode, agents). Deletes everything by default."
         ),
     ] = None,
     target_dir: Annotated[
         str, typer.Option("--target", "-t", help="Target directory to delete from")
     ] = ".",
+    everything: Annotated[
+        bool,
+        typer.Option(
+            "--everything",
+            help="Delete all instruction files, not just those generated from local sources.",
+        ),
+    ] = False,
     yes: Annotated[
         bool,
         typer.Option(
@@ -64,17 +127,25 @@ def delete_main(
 ):
     """Remove downloaded LLM instruction files.
 
-    This command removes files and directories that were downloaded by the 'download' command.
-    It will show you what will be deleted and ask for confirmation before proceeding.
+    This command removes files and directories that were downloaded by the 'download' command
+    or generated by the 'explode' command.
+
+    By default, it ONLY deletes files that correspond to your local 'instructions.md' and
+    'commands.md' files. This prevents accidental deletion of manually created files.
+    Use --everything to delete all standard instruction files and directories.
 
     Examples:
 
     \b
-    # Delete everything (with confirmation)
+    # Delete only generated files (safest, default)
     llm_ide_rules delete
 
     \b
-    # Delete only Cursor and Gemini files
+    # Delete ALL instruction files (including manual ones)
+    llm_ide_rules delete --everything
+
+    \b
+    # Delete only Cursor and Gemini files (but only if generated)
     llm_ide_rules delete cursor gemini
 
     \b
@@ -115,9 +186,39 @@ def delete_main(
         instruction_types, target_path
     )
 
+    skipped_files = []
+
+    if not everything:
+        log.info("filtering files to delete based on local sources")
+        generated_files = get_generated_files(target_path)
+
+        # Expand directories to files for granular filtering
+        expanded_files = []
+        for d in dirs_to_delete:
+            expanded_files.extend([f for f in d.rglob("*") if f.is_file()])
+
+        all_candidates = files_to_delete + expanded_files
+
+        # Filter: keep only files that are in the generated set
+        # We compare resolved paths to be safe
+        files_to_delete = [f for f in all_candidates if f.resolve() in generated_files]
+
+        # Identify skipped files (candidates that were NOT in generated set)
+        skipped_files = [
+            f for f in all_candidates if f.resolve() not in generated_files
+        ]
+
+        # We are no longer deleting whole directories in safe mode
+        dirs_to_delete = []
+
     if not dirs_to_delete and not files_to_delete:
         log.info("no files found to delete")
         typer.echo("No matching instruction files found to delete.")
+        if skipped_files:
+            typer.echo(
+                f"\n{len(skipped_files)} files were skipped because they don't match local instructions/commands."
+            )
+            typer.echo("Use --everything to delete them.")
         return
 
     typer.echo("\nThe following files and directories will be deleted:\n")
@@ -137,6 +238,11 @@ def delete_main(
     total_items = len(dirs_to_delete) + len(files_to_delete)
     typer.echo(f"\nTotal: {total_items} items")
 
+    if skipped_files:
+        typer.echo(
+            f"\n(Note: {len(skipped_files)} other files will be preserved. Use --everything to delete them)"
+        )
+
     if not yes:
         typer.echo()
         confirm = typer.confirm("Are you sure you want to delete these files?")

llm_ide_rules/commands/download.py

@@ -46,7 +46,7 @@ def normalize_repo(repo: str) -> str:
 # The directories listed here are what gets created by explode and what delete removes.
 INSTRUCTION_TYPES = {
     "cursor": {
-        "directories": [".cursor"],
+        "directories": [".cursor/rules", ".cursor/commands"],
         "files": [],
         "include_patterns": [],
     },
@@ -56,22 +56,23 @@ INSTRUCTION_TYPES = {
         "include_patterns": [],
     },
     "gemini": {
-        "directories": [".gemini"],
-        "files": ["GEMINI.md"],
+        "directories": [".gemini/commands"],
+        "files": [],
+        "generated_files": [],
         "include_patterns": [],
     },
     "claude": {
-        "directories": [".claude"],
-        "files": ["CLAUDE.md"],
+        "directories": [".claude/commands"],
+        "files": [],
+        "generated_files": ["CLAUDE.md"],
         "include_patterns": [],
     },
     "opencode": {
-        "directories": [".opencode"],
+        "directories": [".opencode/commands"],
         "files": [],
         "include_patterns": [],
     },
-    "agent": {"directories": [], "files": ["AGENT.md"]},
-    "agents": {"directories": [], "files": [], "recursive_files": ["AGENTS.md"]},
+    "agents": {"directories": [], "files": [], "generated_files": ["AGENTS.md"]},
 }
 
 # Default types to download when no specific types are specified
@@ -288,7 +289,7 @@ def download_main(
     instruction_types: Annotated[
         list[str] | None,
         typer.Argument(
-            help="Types of instructions to download (cursor, github, gemini, claude, agent, agents). Downloads everything by default."
+            help="Types of instructions to download (cursor, github, gemini, claude, opencode, agents). Downloads everything by default."
         ),
     ] = None,
     repo: Annotated[
@@ -355,7 +356,10 @@ def download_main(
 
     try:
         # Copy instruction files
-        copied_items = copy_instruction_files(repo_dir, instruction_types, target_path)
+        copied_items = [
+            f"Downloaded: {item}"
+            for item in copy_instruction_files(repo_dir, instruction_types, target_path)
+        ]
 
         # Check for source files (instructions.md, commands.md) and copy them if available
         # These are needed for 'explode' logic
@@ -373,7 +377,7 @@ def download_main(
                     log.info("copying source file", source=str(src), target=str(dst))
                     dst.parent.mkdir(parents=True, exist_ok=True)
                     dst.write_bytes(src.read_bytes())
-                    copied_items.append(source_file)
+                    copied_items.append(f"Downloaded: {source_file}")
                     sources_copied = True
 
         # Generate rule files locally for supported agents
@@ -395,7 +399,7 @@ def download_main(
                         agent=agent,
                         working_dir=target_path,
                     )
-                    copied_items.append(f"(generated) {agent} rules")
+                    copied_items.append(f"Generated: {agent} rules")
                 except Exception as e:
                     log.error("failed to generate rules", agent=agent, error=str(e))
                     typer.echo(
@@ -408,8 +412,23 @@ def download_main(
             for item in copied_items:
                 typer.echo(f"  - {item}")
         else:
-            log.warning("no files were copied or generated")
-            typer.echo("No matching instruction files found in the repository.")
+            log.info("no files were copied or generated")
+
+            # Build list of expected files
+            expected_files = []
+            for inst_type in instruction_types:
+                config = INSTRUCTION_TYPES[inst_type]
+                expected_files.extend(config.get("directories", []))
+                expected_files.extend(config.get("files", []))
+                expected_files.extend(config.get("recursive_files", []))
+
+            error_msg = "No matching instruction files found in the repository."
+            typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
+
+            if expected_files:
+                typer.echo("\nExpected files/directories:", err=True)
+                for expected in expected_files:
+                    typer.echo(f"  - {expected}", err=True)
 
     finally:
         # Clean up temporary directory

llm_ide_rules/commands/explode.py

@@ -54,9 +54,19 @@ def process_unmapped_as_always_apply(
     section_content = replace_header_with_proper_casing(section_content, section_name)
 
     cursor_agent.write_rule(
-        section_content, filename, cursor_rules_dir, glob_pattern=None
+        section_content,
+        filename,
+        cursor_rules_dir,
+        glob_pattern=None,
+        description=section_name,
+    )
+    github_agent.write_rule(
+        section_content,
+        filename,
+        copilot_dir,
+        glob_pattern=None,
+        description=section_name,
     )
-    github_agent.write_rule(section_content, filename, copilot_dir, glob_pattern=None)
 
     return True
 
@@ -88,7 +98,14 @@ def explode_implementation(
     # Initialize only the agents we need
     agents_to_process = []
     if agent == "all":
-        agents_to_process = ["cursor", "github", "claude", "gemini", "opencode"]
+        agents_to_process = [
+            "cursor",
+            "github",
+            "claude",
+            "gemini",
+            "opencode",
+            "agents",
+        ]
     else:
         agents_to_process = [agent]
 
@@ -103,14 +120,14 @@ def explode_implementation(
             # These agents have both rules and commands
             rules_dir = working_dir / agent_instances[agent_name].rules_dir
             commands_dir = working_dir / agent_instances[agent_name].commands_dir
-            rules_dir.mkdir(parents=True, exist_ok=True)
-            commands_dir.mkdir(parents=True, exist_ok=True)
             agent_dirs[agent_name] = {"rules": rules_dir, "commands": commands_dir}
-        else:
+        elif agent_instances[agent_name].commands_dir:
             # claude, gemini, and opencode only have commands
             commands_dir = working_dir / agent_instances[agent_name].commands_dir
-            commands_dir.mkdir(parents=True, exist_ok=True)
             agent_dirs[agent_name] = {"commands": commands_dir}
+        else:
+            # agents has neither rules nor commands dirs (only generates root doc)
+            agent_dirs[agent_name] = {}
 
     input_path = working_dir / input_file
 
@@ -135,7 +152,8 @@ def explode_implementation(
     if any(line.strip() for line in general):
         general_header = """
 ---
-description:
+description: General Instructions
+globs: 
 alwaysApply: true
 ---
 """
@@ -180,6 +198,7 @@ alwaysApply: true
                     filename,
                     agent_dirs["cursor"]["rules"],
                     glob_pattern=None,
+                    description=section_name,
                 )
             elif "github" in agent_instances:
                 agent_instances["github"].write_rule(
@@ -187,6 +206,7 @@ alwaysApply: true
                     filename,
                     agent_dirs["github"]["rules"],
                     glob_pattern=None,
+                    description=section_name,
                 )
         elif glob_pattern != "manual":
             # Has glob pattern = file-specific rule
@@ -196,6 +216,7 @@ alwaysApply: true
                     filename,
                     agent_dirs["cursor"]["rules"],
                     glob_pattern,
+                    description=section_name,
                 )
             if "github" in agent_instances:
                 agent_instances["github"].write_rule(
@@ -203,6 +224,7 @@ alwaysApply: true
                     filename,
                     agent_dirs["github"]["rules"],
                     glob_pattern,
+                    description=section_name,
                 )
 
     # Process commands for all agents
@@ -210,15 +232,21 @@ alwaysApply: true
     command_sections = {}
     if commands_text:
         _, command_sections_data = parse_sections(commands_text)
-        agents = [agent_instances[name] for name in agents_to_process]
+        agents_with_commands = [
+            agent_instances[name]
+            for name in agents_to_process
+            if agent_instances[name].commands_dir
+        ]
         command_dirs = {
-            name: agent_dirs[name]["commands"] for name in agents_to_process
+            name: agent_dirs[name]["commands"]
+            for name in agents_to_process
+            if "commands" in agent_dirs[name]
         }
 
         for section_name, section_data in command_sections_data.items():
             command_sections[section_name] = section_data.content
             process_command_section(
-                section_name, section_data.content, agents, command_dirs
+                section_name, section_data.content, agents_with_commands, command_dirs
             )
 
     # Generate root documentation (CLAUDE.md, GEMINI.md, etc.)
@@ -228,6 +256,7 @@ alwaysApply: true
             rules_sections,
             command_sections,
             working_dir,
+            section_globs=section_globs,
         )
 
     # Build log message and user output based on processed agents
@@ -239,15 +268,37 @@ alwaysApply: true
             log_data[f"{agent_name}_rules"] = str(agent_dirs[agent_name]["rules"])
             log_data[f"{agent_name}_commands"] = str(agent_dirs[agent_name]["commands"])
             created_dirs.append(f".{agent_name}/")
-        else:
+        elif agent_dirs[agent_name]:
+            # Has commands directory
             log_data[f"{agent_name}_commands"] = str(agent_dirs[agent_name]["commands"])
             created_dirs.append(f".{agent_name}/")
+        # else: agent has no directories (e.g., agents which only generates root doc)
 
-    if len(created_dirs) == 1:
-        success_msg = f"Created files in {created_dirs[0]} directory"
-        typer.echo(typer.style(success_msg, fg=typer.colors.GREEN))
+    if "gemini" in agent_instances:
+        if not agent_instances["gemini"].check_agents_md_config(working_dir):
+            typer.secho(
+                "Warning: Gemini CLI configuration missing for AGENTS.md.",
+                fg=typer.colors.YELLOW,
+            )
+            typer.secho(
+                "Run this command to configure it:",
+                fg=typer.colors.YELLOW,
+            )
+            typer.secho(
+                "  gemini config set agent.instructionFile AGENTS.md",
+                fg=typer.colors.YELLOW,
+            )
+
+    if created_dirs:
+        if len(created_dirs) == 1:
+            success_msg = f"Created files in {created_dirs[0]} directory"
+            typer.echo(typer.style(success_msg, fg=typer.colors.GREEN))
+        else:
+            success_msg = f"Created files in {', '.join(created_dirs)} directories"
+            typer.echo(typer.style(success_msg, fg=typer.colors.GREEN))
     else:
-        success_msg = f"Created files in {', '.join(created_dirs)} directories"
+        # No directories created (e.g., agents that only generate root docs)
+        success_msg = "Created root documentation files"
         typer.echo(typer.style(success_msg, fg=typer.colors.GREEN))
 
 

llm_ide_rules/commands/implode.py

@@ -1,12 +1,12 @@
 """Implode command: Bundle rule files into a single instruction file."""
 
-from pathlib import Path
 from typing_extensions import Annotated
 
 import typer
 
 from llm_ide_rules.agents import get_agent
 from llm_ide_rules.log import log
+from llm_ide_rules.utils import find_project_root
 
 
 def cursor(
@@ -17,7 +17,7 @@ def cursor(
     """Bundle Cursor rules into instructions.md and commands into commands.md."""
 
     agent = get_agent("cursor")
-    cwd = Path.cwd()
+    base_dir = find_project_root()
 
     rules_dir = agent.rules_dir
     if not rules_dir:
@@ -30,14 +30,14 @@ def cursor(
         commands_dir=agent.commands_dir,
     )
 
-    rules_path = cwd / rules_dir
+    rules_path = base_dir / rules_dir
     if not rules_path.exists():
         log.error("cursor rules directory not found", rules_dir=str(rules_path))
         error_msg = f"Cursor rules directory not found: {rules_path}"
         typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
         raise typer.Exit(1)
 
-    output_path = cwd / output
+    output_path = base_dir / output
     rules_written = agent.bundle_rules(output_path)
     if rules_written:
         success_msg = f"Bundled cursor rules into {output}"
@@ -46,7 +46,7 @@ def cursor(
         output_path.unlink(missing_ok=True)
         log.info("no cursor rules to bundle")
 
-    commands_output_path = cwd / "commands.md"
+    commands_output_path = base_dir / "commands.md"
     commands_written = agent.bundle_commands(commands_output_path)
     if commands_written:
         success_msg = "Bundled cursor commands into commands.md"
@@ -63,7 +63,7 @@ def github(
     """Bundle GitHub instructions into instructions.md and prompts into commands.md."""
 
     agent = get_agent("github")
-    cwd = Path.cwd()
+    base_dir = find_project_root()
 
     rules_dir = agent.rules_dir
     if not rules_dir:
@@ -76,7 +76,7 @@ def github(
         prompts_dir=agent.commands_dir,
     )
 
-    rules_path = cwd / rules_dir
+    rules_path = base_dir / rules_dir
     if not rules_path.exists():
         log.error(
             "github instructions directory not found", instructions_dir=str(rules_path)
@@ -85,7 +85,7 @@ def github(
         typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
         raise typer.Exit(1)
 
-    output_path = cwd / output
+    output_path = base_dir / output
     instructions_written = agent.bundle_rules(output_path)
     if instructions_written:
         success_msg = f"Bundled github instructions into {output}"
@@ -94,7 +94,7 @@ def github(
         output_path.unlink(missing_ok=True)
         log.info("no github instructions to bundle")
 
-    commands_output_path = cwd / "commands.md"
+    commands_output_path = base_dir / "commands.md"
     prompts_written = agent.bundle_commands(commands_output_path)
     if prompts_written:
         success_msg = "Bundled github prompts into commands.md"
@@ -109,7 +109,7 @@ def claude(
     """Bundle Claude Code commands into commands.md."""
 
     agent = get_agent("claude")
-    cwd = Path.cwd()
+    base_dir = find_project_root()
 
     commands_dir = agent.commands_dir
     if not commands_dir:
@@ -121,7 +121,7 @@ def claude(
         commands_dir=commands_dir,
     )
 
-    commands_path = cwd / commands_dir
+    commands_path = base_dir / commands_dir
     if not commands_path.exists():
         log.error(
             "claude code commands directory not found", commands_dir=str(commands_path)
@@ -130,7 +130,7 @@ def claude(
         typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
         raise typer.Exit(1)
 
-    output_path = cwd / output
+    output_path = base_dir / output
     commands_written = agent.bundle_commands(output_path)
     if commands_written:
         success_msg = f"Bundled claude commands into {output}"
@@ -146,7 +146,7 @@ def gemini(
     """Bundle Gemini CLI commands into commands.md."""
 
     agent = get_agent("gemini")
-    cwd = Path.cwd()
+    base_dir = find_project_root()
 
     commands_dir = agent.commands_dir
     if not commands_dir:
@@ -158,7 +158,7 @@ def gemini(
         commands_dir=commands_dir,
     )
 
-    commands_path = cwd / commands_dir
+    commands_path = base_dir / commands_dir
     if not commands_path.exists():
         log.error(
             "gemini cli commands directory not found", commands_dir=str(commands_path)
@@ -167,7 +167,7 @@ def gemini(
         typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
         raise typer.Exit(1)
 
-    output_path = cwd / output
+    output_path = base_dir / output
     commands_written = agent.bundle_commands(output_path)
     if commands_written:
         success_msg = f"Bundled gemini commands into {output}"
@@ -183,7 +183,7 @@ def opencode(
     """Bundle OpenCode commands into commands.md."""
 
     agent = get_agent("opencode")
-    cwd = Path.cwd()
+    base_dir = find_project_root()
 
     commands_dir = agent.commands_dir
     if not commands_dir:
@@ -195,7 +195,7 @@ def opencode(
         commands_dir=commands_dir,
     )
 
-    commands_path = cwd / commands_dir
+    commands_path = base_dir / commands_dir
     if not commands_path.exists():
         log.error(
             "opencode commands directory not found", commands_dir=str(commands_path)
@@ -204,7 +204,7 @@ def opencode(
         typer.echo(typer.style(error_msg, fg=typer.colors.RED), err=True)
         raise typer.Exit(1)
 
-    output_path = cwd / output
+    output_path = base_dir / output
     commands_written = agent.bundle_commands(output_path)
     if commands_written:
         success_msg = f"Bundled opencode commands into {output}"

llm_ide_rules/commands/mcp.py

@@ -23,7 +23,7 @@ def explode(
         "all",
         "--agent",
         "-a",
-        help="Agent: claude, cursor, gemini, opencode, copilot, or all",
+        help="Agent: claude, cursor, gemini, opencode, copilot, vscode, or all",
     ),
 ) -> None:
     """Convert unified mcp.json to platform-specific configs."""

llm_ide_rules/constants.py

@@ -1,6 +1,6 @@
 """Shared constants for explode and implode functionality."""
 
-VALID_AGENTS = ["cursor", "github", "claude", "gemini", "opencode", "all"]
+VALID_AGENTS = ["cursor", "github", "claude", "gemini", "opencode", "agents", "all"]
 
 
 def header_to_filename(header: str) -> str: