cite-agent 1.3.7__py3-none-any.whl → 1.3.8__py3-none-any.whl

cite_agent/__version__.py

@@ -1 +1 @@
-__version__ = "1.3.7"
+__version__ = "1.3.8"

cite_agent/enhanced_ai_agent.py

@@ -1003,7 +1003,17 @@ class EnhancedNocturnalAgent:
         capability_lines.append("• You can SEARCH user's paper collection")
         capability_lines.append("• You can COPY text to user's clipboard")
         capability_lines.append("• User's query history is automatically tracked")
-        
+
+        # Add file operation capabilities (Claude Code / Cursor parity)
+        capability_lines.append("")
+        capability_lines.append("📁 DIRECT FILE OPERATIONS (Always available):")
+        capability_lines.append("• read_file(path) - Read files with line numbers (like cat but better)")
+        capability_lines.append("• write_file(path, content) - Create/overwrite files directly")
+        capability_lines.append("• edit_file(path, old, new) - Surgical find/replace edits")
+        capability_lines.append("• glob_search(pattern) - Fast file search (e.g., '**/*.py')")
+        capability_lines.append("• grep_search(pattern) - Fast content search in files")
+        capability_lines.append("• batch_edit_files(edits) - Multi-file refactoring")
+
         sections.append("Capabilities in play:\n" + "\n".join(capability_lines))
 
         # ENHANCED TRUTH-SEEKING RULES (adapt based on mode)
@@ -1098,6 +1108,48 @@ class EnhancedNocturnalAgent:
             "• Example: 'I found 3 papers. I can save them to your library or export to BibTeX if you'd like.'",
         ]
         rules.extend(workflow_rules)
+
+        # Add file operation tool usage rules (CRITICAL for Claude Code parity)
+        file_ops_rules = [
+            "",
+            "📁 FILE OPERATION TOOL USAGE (Use these INSTEAD of shell commands):",
+            "",
+            "🔴 ALWAYS PREFER (in order):",
+            "1. read_file(path) → INSTEAD OF: cat, head, tail",
+            "2. write_file(path, content) → INSTEAD OF: echo >, cat << EOF, printf >",
+            "3. edit_file(path, old, new) → INSTEAD OF: sed, awk",
+            "4. glob_search(pattern, path) → INSTEAD OF: find, ls",
+            "5. grep_search(pattern, path, file_pattern) → INSTEAD OF: grep -r",
+            "",
+            "✅ CORRECT USAGE:",
+            "• Reading code: result = read_file('app.py')",
+            "• Creating file: write_file('config.json', '{...}')",
+            "• Editing code: edit_file('main.py', 'old_var', 'new_var', replace_all=True)",
+            "• Finding files: glob_search('**/*.py', '/home/user/project')",
+            "• Searching code: grep_search('class.*Agent', '.', '*.py', output_mode='content')",
+            "• Multi-file refactor: batch_edit_files([{file: 'a.py', old: '...', new: '...'}, ...])",
+            "",
+            "❌ ANTI-PATTERNS (Don't do these):",
+            "• DON'T use cat when read_file exists",
+            "• DON'T use echo > when write_file exists",
+            "• DON'T use sed when edit_file exists",
+            "• DON'T use find when glob_search exists",
+            "• DON'T use grep -r when grep_search exists",
+            "",
+            "🎯 WHY USE THESE TOOLS:",
+            "• read_file() shows line numbers (critical for code analysis)",
+            "• write_file() handles escaping/quoting automatically (no heredoc hell)",
+            "• edit_file() validates changes before applying (safer than sed)",
+            "• glob_search() is faster and cleaner than find",
+            "• grep_search() returns structured data (easier to parse)",
+            "",
+            "⚠️ SHELL COMMANDS ONLY FOR:",
+            "• System operations (ps, df, du, uptime)",
+            "• Git commands (git status, git diff, git log)",
+            "• Package installs (pip install, Rscript -e \"install.packages(...)\")",
+            "• Running Python/R scripts (python script.py, Rscript analysis.R)",
+        ]
+        rules.extend(file_ops_rules)
         
         sections.append("CRITICAL RULES:\n" + "\n".join(rules))
         
@@ -2191,10 +2243,478 @@ class EnhancedNocturnalAgent:
             
             output = '\n'.join(output_lines).strip()
             return output if output else "Command executed (no output)"
-            
+
         except Exception as e:
             return f"ERROR: {e}"
 
+    # ========================================================================
+    # DIRECT FILE OPERATIONS (Claude Code / Cursor Parity)
+    # ========================================================================
+
+    def read_file(self, file_path: str, offset: int = 0, limit: int = 2000) -> str:
+        """
+        Read file with line numbers (like Claude Code's Read tool)
+
+        Args:
+            file_path: Path to file
+            offset: Starting line number (0-indexed)
+            limit: Maximum number of lines to read
+
+        Returns:
+            File contents with line numbers in format: "  123→content"
+        """
+        try:
+            # Expand ~ to home directory
+            file_path = os.path.expanduser(file_path)
+
+            # Make absolute if relative
+            if not os.path.isabs(file_path):
+                file_path = os.path.abspath(file_path)
+
+            with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                lines = f.readlines()
+
+            # Apply offset and limit
+            if offset or limit:
+                lines = lines[offset:offset+limit if limit else None]
+
+            # Format with line numbers (1-indexed, like vim/editors)
+            numbered_lines = [
+                f"{offset+i+1:6d}→{line.rstrip()}\n"
+                for i, line in enumerate(lines)
+            ]
+
+            result = ''.join(numbered_lines)
+
+            # Update file context
+            self.file_context['last_file'] = file_path
+            if file_path not in self.file_context['recent_files']:
+                self.file_context['recent_files'].append(file_path)
+                self.file_context['recent_files'] = self.file_context['recent_files'][-5:]
+
+            return result if result else "(empty file)"
+
+        except FileNotFoundError:
+            return f"ERROR: File not found: {file_path}"
+        except PermissionError:
+            return f"ERROR: Permission denied: {file_path}"
+        except IsADirectoryError:
+            return f"ERROR: {file_path} is a directory, not a file"
+        except Exception as e:
+            return f"ERROR: {type(e).__name__}: {e}"
+
+    def write_file(self, file_path: str, content: str) -> Dict[str, Any]:
+        """
+        Write file directly (like Claude Code's Write tool)
+        Creates new file or overwrites existing one.
+
+        Args:
+            file_path: Path to file
+            content: Full file content
+
+        Returns:
+            {"success": bool, "message": str, "bytes_written": int}
+        """
+        try:
+            # Expand ~ to home directory
+            file_path = os.path.expanduser(file_path)
+
+            # Make absolute if relative
+            if not os.path.isabs(file_path):
+                file_path = os.path.abspath(file_path)
+
+            # Create parent directories if needed
+            parent_dir = os.path.dirname(file_path)
+            if parent_dir and not os.path.exists(parent_dir):
+                os.makedirs(parent_dir, exist_ok=True)
+
+            # Write file
+            with open(file_path, 'w', encoding='utf-8') as f:
+                bytes_written = f.write(content)
+
+            # Update file context
+            self.file_context['last_file'] = file_path
+            if file_path not in self.file_context['recent_files']:
+                self.file_context['recent_files'].append(file_path)
+                self.file_context['recent_files'] = self.file_context['recent_files'][-5:]
+
+            return {
+                "success": True,
+                "message": f"Wrote {bytes_written} bytes to {file_path}",
+                "bytes_written": bytes_written
+            }
+
+        except PermissionError:
+            return {
+                "success": False,
+                "message": f"ERROR: Permission denied: {file_path}",
+                "bytes_written": 0
+            }
+        except Exception as e:
+            return {
+                "success": False,
+                "message": f"ERROR: {type(e).__name__}: {e}",
+                "bytes_written": 0
+            }
+
+    def edit_file(self, file_path: str, old_string: str, new_string: str,
+                  replace_all: bool = False) -> Dict[str, Any]:
+        """
+        Surgical file edit (like Claude Code's Edit tool)
+
+        Args:
+            file_path: Path to file
+            old_string: Exact string to replace (must be unique unless replace_all=True)
+            new_string: Replacement string
+            replace_all: If True, replace all occurrences. If False, old_string must be unique.
+
+        Returns:
+            {"success": bool, "message": str, "replacements": int}
+        """
+        try:
+            # Expand ~ to home directory
+            file_path = os.path.expanduser(file_path)
+
+            # Make absolute if relative
+            if not os.path.isabs(file_path):
+                file_path = os.path.abspath(file_path)
+
+            # Read file
+            with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                content = f.read()
+
+            # Check if old_string exists
+            if old_string not in content:
+                return {
+                    "success": False,
+                    "message": f"ERROR: old_string not found in {file_path}",
+                    "replacements": 0
+                }
+
+            # Check uniqueness if not replace_all
+            occurrences = content.count(old_string)
+            if not replace_all and occurrences > 1:
+                return {
+                    "success": False,
+                    "message": f"ERROR: old_string appears {occurrences} times in {file_path}. Use replace_all=True or provide more context to make it unique.",
+                    "replacements": 0
+                }
+
+            # Perform replacement
+            if replace_all:
+                new_content = content.replace(old_string, new_string)
+            else:
+                new_content = content.replace(old_string, new_string, 1)
+
+            # Write back
+            with open(file_path, 'w', encoding='utf-8') as f:
+                f.write(new_content)
+
+            # Update file context
+            self.file_context['last_file'] = file_path
+
+            return {
+                "success": True,
+                "message": f"Replaced {occurrences if replace_all else 1} occurrence(s) in {file_path}",
+                "replacements": occurrences if replace_all else 1
+            }
+
+        except FileNotFoundError:
+            return {
+                "success": False,
+                "message": f"ERROR: File not found: {file_path}",
+                "replacements": 0
+            }
+        except PermissionError:
+            return {
+                "success": False,
+                "message": f"ERROR: Permission denied: {file_path}",
+                "replacements": 0
+            }
+        except Exception as e:
+            return {
+                "success": False,
+                "message": f"ERROR: {type(e).__name__}: {e}",
+                "replacements": 0
+            }
+
+    def glob_search(self, pattern: str, path: str = ".") -> Dict[str, Any]:
+        """
+        Fast file pattern matching (like Claude Code's Glob tool)
+
+        Args:
+            pattern: Glob pattern (e.g., "*.py", "**/*.md", "src/**/*.ts")
+            path: Starting directory (default: current directory)
+
+        Returns:
+            {"files": List[str], "count": int, "pattern": str}
+        """
+        try:
+            import glob as glob_module
+
+            # Expand ~ to home directory
+            path = os.path.expanduser(path)
+
+            # Make absolute if relative
+            if not os.path.isabs(path):
+                path = os.path.abspath(path)
+
+            # Combine path and pattern
+            full_pattern = os.path.join(path, pattern)
+
+            # Find matches (recursive if ** in pattern)
+            matches = glob_module.glob(full_pattern, recursive=True)
+
+            # Filter to files only (not directories)
+            files = [f for f in matches if os.path.isfile(f)]
+
+            # Sort by modification time (newest first)
+            files.sort(key=lambda f: os.path.getmtime(f), reverse=True)
+
+            return {
+                "files": files,
+                "count": len(files),
+                "pattern": full_pattern
+            }
+
+        except Exception as e:
+            return {
+                "files": [],
+                "count": 0,
+                "pattern": pattern,
+                "error": f"{type(e).__name__}: {e}"
+            }
+
+    def grep_search(self, pattern: str, path: str = ".",
+                    file_pattern: str = "*",
+                    output_mode: str = "files_with_matches",
+                    context_lines: int = 0,
+                    ignore_case: bool = False,
+                    max_results: int = 100) -> Dict[str, Any]:
+        """
+        Fast content search (like Claude Code's Grep tool / ripgrep)
+
+        Args:
+            pattern: Regex pattern to search for
+            path: Directory to search in
+            file_pattern: Glob pattern for files to search (e.g., "*.py")
+            output_mode: "files_with_matches", "content", or "count"
+            context_lines: Lines of context around matches
+            ignore_case: Case-insensitive search
+            max_results: Maximum number of results to return
+
+        Returns:
+            Depends on output_mode:
+            - files_with_matches: {"files": List[str], "count": int}
+            - content: {"matches": {file: [(line_num, line_content), ...]}}
+            - count: {"counts": {file: match_count}}
+        """
+        try:
+            import re
+
+            # Expand ~ to home directory
+            path = os.path.expanduser(path)
+
+            # Make absolute if relative
+            if not os.path.isabs(path):
+                path = os.path.abspath(path)
+
+            # Compile regex
+            flags = re.IGNORECASE if ignore_case else 0
+            regex = re.compile(pattern, flags)
+
+            # Find files to search
+            glob_result = self.glob_search(file_pattern, path)
+            files_to_search = glob_result["files"]
+
+            # Search each file
+            if output_mode == "files_with_matches":
+                matching_files = []
+                for file_path in files_to_search[:max_results]:
+                    try:
+                        with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                            content = f.read()
+                        if regex.search(content):
+                            matching_files.append(file_path)
+                    except:
+                        continue
+
+                return {
+                    "files": matching_files,
+                    "count": len(matching_files),
+                    "pattern": pattern
+                }
+
+            elif output_mode == "content":
+                matches = {}
+                for file_path in files_to_search:
+                    try:
+                        with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                            lines = f.readlines()
+
+                        file_matches = []
+                        for line_num, line in enumerate(lines, 1):
+                            if regex.search(line):
+                                file_matches.append((line_num, line.rstrip()))
+
+                                if len(file_matches) >= max_results:
+                                    break
+
+                        if file_matches:
+                            matches[file_path] = file_matches
+                    except:
+                        continue
+
+                return {
+                    "matches": matches,
+                    "file_count": len(matches),
+                    "pattern": pattern
+                }
+
+            elif output_mode == "count":
+                counts = {}
+                for file_path in files_to_search:
+                    try:
+                        with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                            content = f.read()
+
+                        match_count = len(regex.findall(content))
+                        if match_count > 0:
+                            counts[file_path] = match_count
+                    except:
+                        continue
+
+                return {
+                    "counts": counts,
+                    "total_matches": sum(counts.values()),
+                    "pattern": pattern
+                }
+
+            else:
+                return {
+                    "error": f"Invalid output_mode: {output_mode}. Use 'files_with_matches', 'content', or 'count'."
+                }
+
+        except re.error as e:
+            return {
+                "error": f"Invalid regex pattern: {e}"
+            }
+        except Exception as e:
+            return {
+                "error": f"{type(e).__name__}: {e}"
+            }
+
+    async def batch_edit_files(self, edits: List[Dict[str, str]]) -> Dict[str, Any]:
+        """
+        Apply multiple file edits atomically (all-or-nothing)
+
+        Args:
+            edits: List of edit operations:
+                [
+                    {"file": "path.py", "old": "...", "new": "..."},
+                    {"file": "other.py", "old": "...", "new": "...", "replace_all": True},
+                    ...
+                ]
+
+        Returns:
+            {
+                "success": bool,
+                "results": {file: {"success": bool, "message": str, "replacements": int}},
+                "total_edits": int,
+                "failed_edits": int
+            }
+        """
+        try:
+            results = {}
+
+            # Phase 1: Validate all edits
+            for edit in edits:
+                file_path = edit["file"]
+                old_string = edit["old"]
+                replace_all = edit.get("replace_all", False)
+
+                # Expand path
+                file_path = os.path.expanduser(file_path)
+                if not os.path.isabs(file_path):
+                    file_path = os.path.abspath(file_path)
+
+                # Check file exists
+                if not os.path.exists(file_path):
+                    return {
+                        "success": False,
+                        "results": {},
+                        "total_edits": 0,
+                        "failed_edits": len(edits),
+                        "error": f"Validation failed: {file_path} not found. No edits applied."
+                    }
+
+                # Check old_string exists
+                try:
+                    with open(file_path, 'r', encoding='utf-8', errors='replace') as f:
+                        content = f.read()
+
+                    if old_string not in content:
+                        return {
+                            "success": False,
+                            "results": {},
+                            "total_edits": 0,
+                            "failed_edits": len(edits),
+                            "error": f"Validation failed: Pattern not found in {file_path}. No edits applied."
+                        }
+
+                    # Check uniqueness if not replace_all
+                    if not replace_all and content.count(old_string) > 1:
+                        return {
+                            "success": False,
+                            "results": {},
+                            "total_edits": 0,
+                            "failed_edits": len(edits),
+                            "error": f"Validation failed: Pattern appears {content.count(old_string)} times in {file_path}. Use replace_all or provide more context. No edits applied."
+                        }
+                except Exception as e:
+                    return {
+                        "success": False,
+                        "results": {},
+                        "total_edits": 0,
+                        "failed_edits": len(edits),
+                        "error": f"Validation failed reading {file_path}: {e}. No edits applied."
+                    }
+
+            # Phase 2: Apply all edits (validation passed)
+            for edit in edits:
+                file_path = edit["file"]
+                old_string = edit["old"]
+                new_string = edit["new"]
+                replace_all = edit.get("replace_all", False)
+
+                result = self.edit_file(file_path, old_string, new_string, replace_all)
+                results[file_path] = result
+
+            # Count successes/failures
+            successful_edits = sum(1 for r in results.values() if r["success"])
+            failed_edits = len(edits) - successful_edits
+
+            return {
+                "success": failed_edits == 0,
+                "results": results,
+                "total_edits": len(edits),
+                "successful_edits": successful_edits,
+                "failed_edits": failed_edits
+            }
+
+        except Exception as e:
+            return {
+                "success": False,
+                "results": {},
+                "total_edits": 0,
+                "failed_edits": len(edits),
+                "error": f"Batch edit failed: {type(e).__name__}: {e}"
+            }
+
+    # ========================================================================
+    # END DIRECT FILE OPERATIONS
+    # ========================================================================
+
     def _classify_command_safety(self, cmd: str) -> str:
         """
         Classify command by safety level for smart execution.
@@ -2795,6 +3315,8 @@ IMPORTANT RULES:
 8. For creating files: touch filename OR echo "content" > filename
 9. For creating directories: mkdir dirname
 10. ALWAYS include 2>/dev/null to suppress errors from find
+11. 🚨 MULTI-STEP QUERIES: For queries like "read X and do Y", ONLY generate the FIRST step (reading X). The LLM will handle subsequent steps after seeing the file contents.
+12. 🚨 NEVER use python -m py_compile or other code execution for finding bugs - just read the file with cat/head
 
 Examples:
 "where am i?" → {{"action": "execute", "command": "pwd", "reason": "Show current directory", "updates_context": false}}
@@ -2804,7 +3326,13 @@ Examples:
 "show me calc.R" → {{"action": "execute", "command": "head -100 calc.R", "reason": "Display file contents", "updates_context": true}}
 "create test directory" → {{"action": "execute", "command": "mkdir test && echo 'Created test/'", "reason": "Create new directory", "updates_context": true}}
 "create empty config.json" → {{"action": "execute", "command": "touch config.json && echo 'Created config.json'", "reason": "Create empty file", "updates_context": true}}
+"write hello.txt with content Hello World" → {{"action": "execute", "command": "echo 'Hello World' > hello.txt", "reason": "Create file with content", "updates_context": true}}
+"create results.txt with line 1 and line 2" → {{"action": "execute", "command": "echo 'line 1' > results.txt && echo 'line 2' >> results.txt", "reason": "Create file with multiple lines", "updates_context": true}}
+"fix bug in script.py change OLD to NEW" → {{"action": "execute", "command": "sed -i 's/OLD/NEW/g' script.py && echo 'Fixed script.py'", "reason": "Edit file to fix bug", "updates_context": true}}
 "search for TODO in py files" → {{"action": "execute", "command": "grep -n 'TODO' *.py 2>/dev/null", "reason": "Find TODO comments", "updates_context": false}}
+"find all bugs in code" → {{"action": "execute", "command": "grep -rn 'BUG:' . 2>/dev/null", "reason": "Search for bug markers in code", "updates_context": false}}
+"read analyze.py and find bugs" → {{"action": "execute", "command": "head -200 analyze.py", "reason": "Read file to analyze bugs", "updates_context": false}}
+"show me calc.py completely" → {{"action": "execute", "command": "cat calc.py", "reason": "Display entire file", "updates_context": false}}
 "git status" → {{"action": "execute", "command": "git status", "reason": "Check repository status", "updates_context": false}}
 "what's in that file?" + last_file=data.csv → {{"action": "execute", "command": "head -100 data.csv", "reason": "Show file contents", "updates_context": false}}
 "hello" → {{"action": "none", "reason": "Conversational greeting, no command needed"}}
@@ -2851,8 +3379,211 @@ JSON:"""
                                 "reason": "This command could cause system damage"
                             }
                         else:
-                            # Execute the command
-                            output = self.execute_command(command)
+                            # ========================================
+                            # COMMAND INTERCEPTOR: Translate shell commands to file operations
+                            # (Claude Code / Cursor parity)
+                            # ========================================
+                            intercepted = False
+                            output = ""
+
+                            # Check for file reading commands (cat, head, tail)
+                            if command.startswith(('cat ', 'head ', 'tail ')):
+                                import shlex
+                                try:
+                                    parts = shlex.split(command)
+                                    cmd = parts[0]
+
+                                    # Extract filename (last non-flag argument)
+                                    filename = None
+                                    for part in reversed(parts[1:]):
+                                        if not part.startswith('-'):
+                                            filename = part
+                                            break
+
+                                    if filename:
+                                        # Use read_file instead of cat/head/tail
+                                        if cmd == 'head':
+                                            # head -n 100 file OR head file
+                                            limit = 100  # default
+                                            if '-n' in parts or '-' in parts[0]:
+                                                try:
+                                                    idx = parts.index('-n') if '-n' in parts else 0
+                                                    limit = int(parts[idx + 1])
+                                                except:
+                                                    pass
+                                            output = self.read_file(filename, offset=0, limit=limit)
+                                        elif cmd == 'tail':
+                                            # For tail, read last N lines (harder, so just read all and show it's tail)
+                                            output = self.read_file(filename)
+                                            if "ERROR" not in output:
+                                                lines = output.split('\n')
+                                                output = '\n'.join(lines[-100:])  # last 100 lines
+                                        else:  # cat
+                                            output = self.read_file(filename)
+
+                                        intercepted = True
+                                        tools_used.append("read_file")
+                                        if debug_mode:
+                                            print(f"🔄 Intercepted: {command} → read_file({filename})")
+                                except:
+                                    pass  # Fall back to shell execution
+
+                            # Check for file search commands (find)
+                            if not intercepted and 'find' in command and '-name' in command:
+                                try:
+                                    import re
+                                    # Extract pattern: find ... -name '*pattern*'
+                                    name_match = re.search(r"-name\s+['\"]?\*?([^'\"*\s]+)\*?['\"]?", command)
+                                    if name_match:
+                                        pattern = f"**/*{name_match.group(1)}*"
+                                        path_match = re.search(r"find\s+([^\s]+)", command)
+                                        search_path = path_match.group(1) if path_match else "."
+
+                                        result = self.glob_search(pattern, search_path)
+                                        output = '\n'.join(result['files'][:20])  # Show first 20 matches
+                                        intercepted = True
+                                        tools_used.append("glob_search")
+                                        if debug_mode:
+                                            print(f"🔄 Intercepted: {command} → glob_search({pattern}, {search_path})")
+                                except:
+                                    pass
+
+                            # Check for file writing commands (echo > file, grep > file, etc.) - CHECK THIS FIRST!
+                            # This must come BEFORE the plain grep interceptor
+                            if not intercepted and ('>' in command or '>>' in command):
+                                try:
+                                    import re
+
+                                    # Handle grep ... > file (intercept and execute grep, then write output)
+                                    if 'grep' in command and '>' in command:
+                                        # Extract: grep -rn 'pattern' path > output.txt
+                                        grep_match = re.search(r"grep\s+(.*)>\s*(\S+)", command)
+                                        if grep_match:
+                                            grep_part = grep_match.group(1).strip()
+                                            output_file = grep_match.group(2)
+
+                                            # Extract pattern and options from grep command
+                                            pattern_match = re.search(r"['\"]([^'\"]+)['\"]", grep_part)
+                                            if pattern_match:
+                                                pattern = pattern_match.group(1)
+                                                search_path = "."
+                                                file_pattern = "*.py" if "*.py" in command else "*"
+
+                                                if debug_mode:
+                                                    print(f"🔄 Intercepted: {command} → grep_search('{pattern}', '{search_path}', '{file_pattern}') + write_file({output_file})")
+
+                                                # Execute grep_search
+                                                try:
+                                                    grep_result = self.grep_search(
+                                                        pattern=pattern,
+                                                        path=search_path,
+                                                        file_pattern=file_pattern,
+                                                        output_mode="content"
+                                                    )
+
+                                                    # Format matches as text (like grep -rn output)
+                                                    output_lines = []
+                                                    for file_path, matches in grep_result.get('matches', {}).items():
+                                                        for line_num, line_content in matches:
+                                                            output_lines.append(f"{file_path}:{line_num}:{line_content}")
+
+                                                    content_to_write = '\n'.join(output_lines) if output_lines else "(no matches found)"
+
+                                                    # Write grep output to file
+                                                    write_result = self.write_file(output_file, content_to_write)
+                                                    if write_result['success']:
+                                                        output = f"Found {len(output_lines)} lines with '{pattern}' → Created {output_file} ({write_result['bytes_written']} bytes)"
+                                                        intercepted = True
+                                                        tools_used.extend(["grep_search", "write_file"])
+                                                except Exception as e:
+                                                    if debug_mode:
+                                                        print(f"⚠️ Grep > file interception error: {e}")
+                                                    # Fall back to normal execution
+                                                    pass
+
+                                    # Extract: echo 'content' > filename OR cat << EOF > filename
+                                    if not intercepted and 'echo' in command and '>' in command:
+                                        # echo 'content' > file OR echo "content" > file
+                                        match = re.search(r"echo\s+['\"](.+?)['\"].*?>\s*(\S+)", command)
+                                        if match:
+                                            content = match.group(1)
+                                            filename = match.group(2)
+                                            # Unescape common sequences
+                                            content = content.replace('\\n', '\n').replace('\\t', '\t')
+                                            result = self.write_file(filename, content + '\n')
+                                            if result['success']:
+                                                output = f"Created {filename} ({result['bytes_written']} bytes)"
+                                                intercepted = True
+                                                tools_used.append("write_file")
+                                                if debug_mode:
+                                                    print(f"🔄 Intercepted: {command} → write_file({filename}, ...)")
+                                except:
+                                    pass
+
+                            # Check for sed editing commands
+                            if not intercepted and command.startswith('sed '):
+                                try:
+                                    import re
+                                    # sed 's/old/new/g' file OR sed -i 's/old/new/' file
+                                    match = re.search(r"sed.*?['\"]s/([^/]+)/([^/]+)/", command)
+                                    if match:
+                                        old_text = match.group(1)
+                                        new_text = match.group(2)
+                                        # Extract filename (last argument)
+                                        parts = command.split()
+                                        filename = parts[-1]
+
+                                        # Determine if replace_all based on /g flag
+                                        replace_all = '/g' in command
+
+                                        result = self.edit_file(filename, old_text, new_text, replace_all=replace_all)
+                                        if result['success']:
+                                            output = result['message']
+                                            intercepted = True
+                                            tools_used.append("edit_file")
+                                            if debug_mode:
+                                                print(f"🔄 Intercepted: {command} → edit_file({filename}, {old_text}, {new_text})")
+                                except:
+                                    pass
+
+                            # Check for heredoc file creation (cat << EOF > file)
+                            if not intercepted and '<<' in command and ('EOF' in command or 'HEREDOC' in command):
+                                try:
+                                    import re
+                                    # Extract: cat << EOF > filename OR cat > filename << EOF
+                                    # Note: We can't actually get the heredoc content from a single command line
+                                    # This would need to be handled differently (multi-line input)
+                                    # For now, just detect and warn
+                                    if debug_mode:
+                                        print(f"⚠️  Heredoc detected but not intercepted: {command[:80]}")
+                                except:
+                                    pass
+
+                            # Check for content search commands (grep -r) WITHOUT redirection
+                            # This comes AFTER grep > file interceptor to avoid conflicts
+                            if not intercepted and command.startswith('grep ') and ('-r' in command or '-R' in command):
+                                try:
+                                    import re
+                                    # Extract pattern: grep -r 'pattern' path
+                                    pattern_match = re.search(r"grep.*?['\"]([^'\"]+)['\"]", command)
+                                    if pattern_match:
+                                        pattern = pattern_match.group(1)
+                                        # Extract path (last argument usually)
+                                        parts = command.split()
+                                        search_path = parts[-1] if len(parts) > 2 else "."
+
+                                        result = self.grep_search(pattern, search_path, "*.py", output_mode="files_with_matches")
+                                        output = f"Files matching '{pattern}':\n" + '\n'.join(result['files'][:20])
+                                        intercepted = True
+                                        tools_used.append("grep_search")
+                                        if debug_mode:
+                                            print(f"🔄 Intercepted: {command} → grep_search({pattern}, {search_path})")
+                                except:
+                                    pass
+
+                            # If not intercepted, execute as shell command
+                            if not intercepted:
+                                output = self.execute_command(command)
                             
                             if not output.startswith("ERROR"):
                                 # Success - store results
@@ -3245,11 +3976,44 @@ JSON:"""
                     api_results=api_results,
                     tools_used=tools_used
                 )
-                
+
+                # POST-PROCESSING: Auto-extract code blocks and write files if user requested file creation
+                # This fixes the issue where LLM shows corrected code but doesn't create the file
+                if any(keyword in request.question.lower() for keyword in ['create', 'write', 'save', 'generate', 'fixed', 'corrected']):
+                    # Extract filename from query (e.g., "write to foo.py", "create bar_fixed.py")
+                    import re
+                    filename_match = re.search(r'(?:to|create|write|save|generate)\s+(\w+[._-]\w+\.[\w]+)', request.question, re.IGNORECASE)
+                    if not filename_match:
+                        # Try pattern: "foo_fixed.py" or "bar.py"
+                        filename_match = re.search(r'(\w+_fixed\.[\w]+|\w+\.[\w]+)', request.question)
+
+                    if filename_match:
+                        target_filename = filename_match.group(1)
+
+                        # Extract code block from response (```python ... ``` or ``` ... ```)
+                        code_block_pattern = r'```(?:python|bash|sh|r|sql)?\n(.*?)```'
+                        code_blocks = re.findall(code_block_pattern, response.response, re.DOTALL)
+
+                        if code_blocks:
+                            # Use the LARGEST code block (likely the complete file)
+                            largest_block = max(code_blocks, key=len)
+
+                            # Write to file
+                            try:
+                                write_result = self.write_file(target_filename, largest_block)
+                                if write_result['success']:
+                                    # Append confirmation to response
+                                    response.response += f"\n\n✅ File created: {target_filename} ({write_result['bytes_written']} bytes)"
+                                    if debug_mode:
+                                        print(f"🔄 Auto-extracted code block → write_file({target_filename})")
+                            except Exception as e:
+                                if debug_mode:
+                                    print(f"⚠️ Auto-write failed: {e}")
+
                 # CRITICAL: Save to conversation history
                 self.conversation_history.append({"role": "user", "content": request.question})
                 self.conversation_history.append({"role": "assistant", "content": response.response})
-                
+
                 return response
 
             # DEV MODE ONLY: Direct Groq calls (only works with local API keys)

{cite_agent-1.3.7.dist-info → cite_agent-1.3.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cite-agent
-Version: 1.3.7
+Version: 1.3.8
 Summary: Terminal AI assistant for academic research with citation verification
 Home-page: https://github.com/Spectating101/cite-agent
 Author: Cite-Agent Team

{cite_agent-1.3.7.dist-info → cite_agent-1.3.8.dist-info}/RECORD

@@ -1,6 +1,6 @@
 cite_agent/__init__.py,sha256=wAXV2v8nNOmIAd0rh8196ItBl9hHWBVOBl5Re4VB77I,1645
 cite_agent/__main__.py,sha256=6x3lltwG-iZHeQbN12rwvdkPDfd2Rmdk71tOOaC89Mw,179
-cite_agent/__version__.py,sha256=9peaXOar2qezOPJEKG6cD_A0aaXrzdVN8h-v6fBoBEk,22
+cite_agent/__version__.py,sha256=47xEhOdVR5Y8-pZH8aVP6Z2UhhY8jGWTQ-rJHt5fIeU,22
 cite_agent/account_client.py,sha256=yLuzhIJoIZuXHXGbaVMzDxRATQwcy-wiaLnUrDuwUhI,5725
 cite_agent/agent_backend_only.py,sha256=H4DH4hmKhT0T3rQLAb2xnnJVjxl3pOZaljL9r6JndFY,6314
 cite_agent/ascii_plotting.py,sha256=lk8BaECs6fmjtp4iH12G09-frlRehAN7HLhHt2crers,8570
@@ -11,7 +11,7 @@ cite_agent/cli_conversational.py,sha256=RAmgRNRyB8gQ8QLvWU-Tt23j2lmA34rQNT5F3_7S
 cite_agent/cli_enhanced.py,sha256=EAaSw9qtiYRWUXF6_05T19GCXlz9cCSz6n41ASnXIPc,7407
 cite_agent/cli_workflow.py,sha256=4oS_jW9D8ylovXbEFdsyLQONt4o0xxR4Xatfcc4tnBs,11641
 cite_agent/dashboard.py,sha256=VGV5XQU1PnqvTsxfKMcue3j2ri_nvm9Be6O5aVays_w,10502
-cite_agent/enhanced_ai_agent.py,sha256=wyuQu50mZo6jMYZqFD8Bqjk55dFFOBBR28AixchftXY,187083
+cite_agent/enhanced_ai_agent.py,sha256=X-MMgAAezDjIyb3Ro29BeO9zE5-iz-hqjTVhZIBp_GQ,225001
 cite_agent/project_detector.py,sha256=fPl5cLTy_oyufqrQ7RJ5IRVdofZoPqDRaQXW6tRtBJc,6086
 cite_agent/rate_limiter.py,sha256=-0fXx8Tl4zVB4O28n9ojU2weRo-FBF1cJo9Z5jC2LxQ,10908
 cite_agent/session_manager.py,sha256=B0MXSOsXdhO3DlvTG7S8x6pmGlYEDvIZ-o8TZM23niQ,9444
@@ -23,9 +23,9 @@ cite_agent/updater.py,sha256=udoAAN4gBKAvKDV7JTh2FJO_jIhNk9bby4x6n188MEY,8458
 cite_agent/web_search.py,sha256=FZCuNO7MAITiOIbpPbJyt2bzbXPzQla-9amJpnMpW_4,6520
 cite_agent/workflow.py,sha256=a0YC0Mzz4or1C5t2gZcuJBQ0uMOZrooaI8eLu2kkI0k,15086
 cite_agent/workflow_integration.py,sha256=A9ua0DN5pRtuU0cAwrUTGvqt2SXKhEHQbrHx16EGnDM,10910
-cite_agent-1.3.7.dist-info/licenses/LICENSE,sha256=XJkyO4IymhSUniN1ENY6lLrL2729gn_rbRlFK6_Hi9M,1074
-cite_agent-1.3.7.dist-info/METADATA,sha256=YRov18tZiDcm3tnPS7nIPoD8Ruq1wFghllHcqy6mTKc,12231
-cite_agent-1.3.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cite_agent-1.3.7.dist-info/entry_points.txt,sha256=bJ0u28nFIxQKH1PWQ2ak4PV-FAjhoxTC7YADEdDenFw,83
-cite_agent-1.3.7.dist-info/top_level.txt,sha256=NNfD8pxDZzBK8tjDIpCs2BW9Va-OQ5qUFbEx0SgmyIE,11
-cite_agent-1.3.7.dist-info/RECORD,,
+cite_agent-1.3.8.dist-info/licenses/LICENSE,sha256=XJkyO4IymhSUniN1ENY6lLrL2729gn_rbRlFK6_Hi9M,1074
+cite_agent-1.3.8.dist-info/METADATA,sha256=VIfBiOvuEVFBm81jIoNOUsWbOfGq7Rk2jNAPDbzqGaY,12231
+cite_agent-1.3.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cite_agent-1.3.8.dist-info/entry_points.txt,sha256=bJ0u28nFIxQKH1PWQ2ak4PV-FAjhoxTC7YADEdDenFw,83
+cite_agent-1.3.8.dist-info/top_level.txt,sha256=NNfD8pxDZzBK8tjDIpCs2BW9Va-OQ5qUFbEx0SgmyIE,11
+cite_agent-1.3.8.dist-info/RECORD,,