refactor(restructure): git mv all source files into hermes_agent/ package

Pure file moves, zero content changes. Every file in agent/, tools/,
hermes_cli/, gateway/, acp_adapter/, cron/, and plugins/ moves into
hermes_agent/. Top-level modules (run_agent.py, cli.py, etc.) move to
their new homes per the restructure manifest.

Git sees 100% similarity on all moves.

Part of #14182, #14183

tools/binary_extensions.py

@@ -1,42 +0,0 @@
-"""Binary file extensions to skip for text-based operations.
-
-These files can't be meaningfully compared as text and are often large.
-Ported from free-code src/constants/files.ts.
-"""
-
-BINARY_EXTENSIONS = frozenset({
-    # Images
-    ".png", ".jpg", ".jpeg", ".gif", ".bmp", ".ico", ".webp", ".tiff", ".tif",
-    # Videos
-    ".mp4", ".mov", ".avi", ".mkv", ".webm", ".wmv", ".flv", ".m4v", ".mpeg", ".mpg",
-    # Audio
-    ".mp3", ".wav", ".ogg", ".flac", ".aac", ".m4a", ".wma", ".aiff", ".opus",
-    # Archives
-    ".zip", ".tar", ".gz", ".bz2", ".7z", ".rar", ".xz", ".z", ".tgz", ".iso",
-    # Executables/binaries
-    ".exe", ".dll", ".so", ".dylib", ".bin", ".o", ".a", ".obj", ".lib",
-    ".app", ".msi", ".deb", ".rpm",
-    # Documents (exclude .pdf — text-based, agents may want to inspect)
-    ".doc", ".docx", ".xls", ".xlsx", ".ppt", ".pptx",
-    ".odt", ".ods", ".odp",
-    # Fonts
-    ".ttf", ".otf", ".woff", ".woff2", ".eot",
-    # Bytecode / VM artifacts
-    ".pyc", ".pyo", ".class", ".jar", ".war", ".ear", ".node", ".wasm", ".rlib",
-    # Database files
-    ".sqlite", ".sqlite3", ".db", ".mdb", ".idx",
-    # Design / 3D
-    ".psd", ".ai", ".eps", ".sketch", ".fig", ".xd", ".blend", ".3ds", ".max",
-    # Flash
-    ".swf", ".fla",
-    # Lock/profiling data
-    ".lockb", ".dat", ".data",
-})
-
-
-def has_binary_extension(path: str) -> bool:
-    """Check if a file path has a binary extension. Pure string check, no I/O."""
-    dot = path.rfind(".")
-    if dot == -1:
-        return False
-    return path[dot:].lower() in BINARY_EXTENSIONS