docs: update all README files with comprehensive documentation

Update documentation across the project to reflect current state of codebase:
- cli/README.md: Add all commands (codex, gemini, daemon subcommands, doctor, mcp),
  configuration options, storage locations, and source structure references
- server/README.md: Add complete HTTP API reference, Socket.IO events, Telegram bot
  features, core logic descriptions, and source structure
- web/README.md: Add all routes, feature descriptions, authentication flow, data
  fetching, real-time updates, and source structure
- README.md: Improve feature list clarity, add HTTPS exposure instructions in
  quickstart, add multi-agent support section

cli/README.md

@@ -1,56 +1,107 @@
 # hapi CLI
 
-Run Claude Code or Codex sessions from your terminal and control them remotely through the hapi server.
+Run Claude Code, Codex, or Gemini sessions from your terminal and control them remotely through the hapi server.
 
 ## What it does
+
 - Starts Claude Code sessions and registers them with hapi-server.
 - Starts Codex mode for OpenAI-based sessions.
+- Starts Gemini mode via ACP (Anthropic Code Plugins).
 - Provides an MCP stdio bridge for external tools.
 - Manages a background daemon for long-running sessions.
 - Includes diagnostics and auth helpers.
 
 ## Typical flow
+
 1. Start the server and set env vars (see ../server/README.md).
 2. Set the same CLI_API_TOKEN on this machine or run `hapi auth login`.
 3. Run `hapi` to start a session.
 4. Use the web app or Telegram Mini App to monitor and control.
 
-## Quickstart
-```bash
-# Point to the server if it is not on localhost:3006
-export HAPI_BOT_URL="https://your-server-domain"
-
-hapi              # prompts for CLI_API_TOKEN and saves it locally
-```
-
 ## Commands
-- `hapi` - start a Claude Code session (passes through Claude CLI flags)
-- `hapi codex` - start Codex mode
-- `hapi mcp` - start MCP stdio bridge
-- `hapi auth` - login/status/logout for CLI_API_TOKEN
-- `hapi server` - start the bundled server (single binary workflow)
-- `hapi daemon` - manage background service
-- `hapi doctor` - diagnostics and cleanup
+
+### Session commands
+
+- `hapi` - Start a Claude Code session (passes through Claude CLI flags). See `src/index.ts`.
+- `hapi codex` - Start Codex mode. See `src/codex/runCodex.ts`.
+- `hapi gemini` - Start Gemini mode via ACP. See `src/agent/runners/runAgentSession.ts`.
+
+### Authentication
+
+- `hapi auth status` - Show authentication configuration and token source.
+- `hapi auth login` - Interactively enter and save CLI_API_TOKEN.
+- `hapi auth logout` - Clear saved credentials.
+
+See `src/commands/auth.ts`.
+
+### Daemon management
+
+- `hapi daemon start` - Start daemon as detached process.
+- `hapi daemon stop` - Stop daemon gracefully.
+- `hapi daemon status` - Show daemon diagnostics.
+- `hapi daemon list` - List active sessions managed by daemon.
+- `hapi daemon stop-session <sessionId>` - Terminate specific session.
+- `hapi daemon logs` - Print path to latest daemon log file.
+- `hapi daemon install` - Install daemon as system service.
+- `hapi daemon uninstall` - Remove daemon system service.
+
+See `src/daemon/run.ts`.
+
+### Diagnostics
+
+- `hapi doctor` - Show full diagnostics (version, daemon status, logs, processes).
+- `hapi doctor clean` - Kill runaway HAPI processes.
+
+See `src/ui/doctor.ts`.
+
+### Other
+
+- `hapi mcp` - Start MCP stdio bridge. See `src/codex/happyMcpStdioBridge.ts`.
+- `hapi server` - Start the bundled server (single binary workflow).
 
 ## Configuration
-Required:
-- `CLI_API_TOKEN` - shared secret; must match the server
-- `HAPI_BOT_URL` - server base URL (default: http://localhost:3006)
 
-`CLI_API_TOKEN` can be set via env or stored in `~/.hapi/settings.json` (env wins).
+See `src/configuration.ts` for all options.
 
-Optional:
-- `HAPI_HOME` - config/data directory (default: ~/.hapi)
-- `HAPI_EXPERIMENTAL` - enable experimental features (true/1/yes)
-- `HAPI_HTTP_MCP_URL` - default MCP target for `hapi mcp`
-- `HAPI_CLAUDE_PATH` - path to a specific `claude` executable
+### Required
+
+- `CLI_API_TOKEN` - Shared secret; must match the server. Can be set via env or `~/.hapi/settings.json` (env wins).
+- `HAPI_BOT_URL` - Server base URL (default: http://localhost:3006).
+
+### Optional
+
+- `HAPI_HOME` - Config/data directory (default: ~/.hapi).
+- `HAPI_EXPERIMENTAL` - Enable experimental features (true/1/yes).
+- `HAPI_CLAUDE_PATH` - Path to a specific `claude` executable.
+- `HAPI_HTTP_MCP_URL` - Default MCP target for `hapi mcp`.
+
+### Daemon
+
+- `HAPI_DAEMON_HEARTBEAT_INTERVAL` - Heartbeat interval in ms (default: 60000).
+- `HAPI_DAEMON_HTTP_TIMEOUT` - HTTP timeout for daemon control in ms (default: 10000).
+
+### Gemini/Agent
+
+- `HAPPY_GEMINI_COMMAND` - Gemini executable command (default: gemini).
+- `HAPPY_GEMINI_ARGS` - Gemini arguments (default: --acp).
+
+## Storage
+
+Data is stored in `~/.hapi/` (or `$HAPI_HOME`):
+
+- `settings.json` - User settings (machineId, token, onboarding flag). See `src/persistence.ts`.
+- `daemon.state.json` - Daemon state (pid, port, version, heartbeat).
+- `logs/` - Log files.
 
 ## Requirements
+
 - Claude CLI installed and logged in (`claude` on PATH).
 - Bun for building from source.
 
 ## Build from source
+
 From the repo root:
+
 ```bash
 bun install
 bun run build:cli
@@ -58,10 +109,23 @@ bun run build:cli:exe
 ```
 
 For an all-in-one binary that also embeds the web app:
+
 ```bash
 bun run build:single-exe
 ```
 
+## Source structure
+
+- `src/api/` - Bot communication (Socket.IO + REST).
+- `src/claude/` - Claude Code integration.
+- `src/codex/` - Codex mode integration.
+- `src/agent/` - Multi-agent support (Gemini via ACP).
+- `src/daemon/` - Background service.
+- `src/commands/` - CLI command handlers.
+- `src/ui/` - User interface and diagnostics.
+- `src/modules/` - Tool implementations (ripgrep, difftastic, git).
+
 ## Related docs
+
 - `../server/README.md`
 - `../web/README.md`