Update configuration files and remove deprecated scripts

- Updated `Cargo.lock` and `Cargo.toml` to reflect new dependency versions and unified configuration paths.
- Added a new `tools` member to the workspace for configuration management.
- Removed obsolete scripts (`fix_json.py`, `install_mcp_servers.sh`, `mcpd_wrapper_fixed.sh`, `mcpd_wrapper_patch.sh`, `rebuild_cli.sh`, `rebuild_mcp_servers.sh`, and `updated_servers.json`) to streamline the project.
- Enhanced the installation script to create a configuration directory and provide clearer next steps for users.
- Updated documentation in `README.md` and other files to reflect changes in configuration paths and usage instructions.

Author: frostdev-ops

.cursor/rules/02-cli.mdc

@@ -13,8 +13,8 @@ The primary user interface is provided by the `gemini-cli` crate ([cli/README.md
 *   **Wrapper:** The `gemini` command (usually installed via `install.sh` to `~/.bashrc` or `~/.zshrc`) is a crucial wrapper around `gemini-cli-bin` that manages session environment variables (`GEMINI_SESSION_ID`) for history persistence across separate command invocations. See the wrapper function definition in [README.md](mdc:README.md).
 *   **Dependencies:** Leverages `gemini-core` for API communication, `gemini-mcp` for tool integration, and `gemini-memory` for memory features.
 *   **Configuration:**
-    *   `~/.config/gemini-cli/config.toml`: Stores API key, default model, system prompt, feature flags (history, memory). Managed via `gemini --set-...` flags or manual editing. See [cli/README.md](mdc:cli/README.md) for details.
-    *   `~/.config/gemini-cli/mcp_servers.json`: Configures connections to MCP servers (used by the embedded MCP host or the `mcp-hostd` daemon). See [mcp/README.md](mdc:mcp/README.md).
+    *   `~/.config/gemini-suite/config.toml`: Stores API key, default model, system prompt, feature flags (history, memory broker, auto memory). Managed via `gemini --set-...` flags or manual editing. See [cli/README.md](mdc:cli/README.md).
+    *   `~/.config/gemini-suite/mcp_servers.json`: Configures connections to MCP servers (used by the embedded MCP host or the `mcp-hostd` daemon). See [mcp/README.md](mdc:mcp/README.md).
 *   **Interaction Modes:** Supports single-shot prompts (default), interactive chat (`-i`), task loops (`-t`), and combined interactive task mode (`-i -t`). These are detailed in [INTERACTIVE-TASKS.md](mdc:INTERACTIVE-TASKS.md).
-*   **History:** Saved in `~/.local/share/gemini-cli/history/`. Requires the wrapper function for history across commands.
+*   **History:** Saved in `~/.local/share/gemini-suite/history/`. Requires the wrapper function for history across commands.
 *   **Built-in Server Execution:** Can run built-in MCP servers directly via flags (`--filesystem-mcp`, `--command-mcp`, `--memory-store-mcp`).

.cursor/rules/03-mcp.mdc

@@ -13,7 +13,7 @@ MCP allows Gemini to use external tools and services. This is primarily handled
     *   Can run embedded within the CLI.
     *   Can run as a standalone daemon: `mcp-hostd` ([mcp/src/bin/mcp-hostd.rs](mdc:mcp/src/bin/mcp-hostd.rs)).
 *   **MCP Servers:** External processes providing tools (capabilities). The host connects to them based on configuration.
-    *   **Configuration:** Defined in `~/.config/gemini-cli/mcp_servers.json`. Specifies server name, transport (stdio, sse, websocket), command to launch (for stdio), etc. See [mcp/README.md](mdc:mcp/README.md) for format.
+    *   **Configuration:** Defined in `~/.config/gemini-suite/mcp_servers.json`. Specifies server name, transport (stdio, sse, websocket), command to launch (for stdio), etc. See [mcp/README.md](mdc:mcp/README.md) for format.
     *   **Transports:** Supports `Stdio`, `SSE`, and `WebSocket`.
     *   **Communication:** Uses JSON-RPC 2.0.
 *   **Built-in Servers:** The source code for common servers is included within `gemini-mcp`:

.cursor/rules/04-memory.mdc

@@ -13,7 +13,7 @@ Persistent, semantic memory is managed by the `gemini-memory` crate ([memory/REA
 *   **`Memory` Struct ([memory/src/memory.rs](mdc:memory/src/memory.rs))**: Represents a single memory item (key, value, timestamp, tags, metadata, vector embedding).
 *   **LanceDB Integration:**
     *   Uses LanceDB ([https://lancedb.com/](mdc:https:/lancedb.com)) as the vector database for efficient storage and semantic search.
-    *   Database typically located at `~/.local/share/gemini-cli/memory.db` ([memory/src/config.rs](mdc:memory/src/config.rs)).
+    *   Database typically located at `~/.local/share/gemini-suite/memory.db` ([memory/src/config.rs](mdc:memory/src/config.rs)).
     *   Schema defined using Apache Arrow ([memory/src/schema.rs](mdc:memory/src/schema.rs)), including a vector column.
     *   CRUD operations and vector search are implemented using the LanceDB Rust SDK.
 *   **Embeddings via MCP:**

Cargo.lock

@@ -10,6 +10,7 @@ members = [
     "happe",     # Host Application Environment daemon (Placeholder)
     "install",   # Installer crate for Gemini CLI Suite
     "daemon-manager", # CLI for managing gemini-suite daemons and MCP servers
+    "tools",     # Tools for configuration, maintenance, etc.
 ]
 
 [workspace.lints]

Cargo.toml

@@ -178,31 +178,26 @@ The suite uses a couple of configuration files, primarily managed by the CLI:
 
 ### CLI Configuration (`config.toml`)
 
-*   **Location:** `~/.config/gemini-cli/config.toml`
-*   **Content:** Stores API key, default system prompt, default model name, and feature flags (history, memory broker, auto memory).
-*   **Management:** Use the `gemini` command with flags:
-    *   `gemini --set-api-key YOUR_API_KEY_HERE`
-    *   `gemini --set-system-prompt "Your desired prompt"`
-    *   `gemini --set-model "gemini-1.5-pro-latest"`
-    *   `gemini --show-config`
-    *   Or edit the file manually.
+*   **Location:** `~/.config/gemini-suite/config.toml`
+*   **Purpose:** Unified configuration for CLI, Daemons (HAPPE, IDA, mcp-hostd).
+*   **Managed by:** `gemini config` or `gemini daemon-manager config` subcommands.
+*   **Details:** See `cli/README.md` and `daemon-manager/README.md`.
 
 ### MCP Server Configuration (`mcp_servers.json`)
 
-*   **Location:** `~/.config/gemini-cli/mcp_servers.json`
-*   **Content:** Defines how the MCP host (either `mcp-hostd` daemon or the one embedded in the CLI) should connect to MCP servers (built-in or external).
-*   **Format:** JSON array of server objects. See the `gemini-mcp` README for details.
-*   **Management:** Edit the file manually. The `install.sh` script may set up initial entries for built-in servers.
+*   **Location:** `~/.config/gemini-suite/mcp_servers.json`
+*   **Purpose:** Defines how the MCP Host connects to external tool servers.
+*   **Managed by:** `gemini mcp` or `gemini daemon-manager mcp` subcommands.
 
 ### API Key Precedence 🔑
 
-1.  Value in `~/.config/gemini-cli/config.toml`.
+1.  Value in `~/.config/gemini-suite/config.toml`.
 2.  `GEMINI_API_KEY` environment variable.
 3.  Value in a `.env` file in the current working directory (or project root during development).
 
 ### System Prompt Precedence 🗣️
 
-1.  Value in `~/.config/gemini-cli/config.toml`.
+1.  Value in `~/.config/gemini-suite/config.toml`.
 2.  Default prompt embedded in the CLI.
 
 ## 💡 CLI Usage
@@ -256,14 +251,12 @@ mcpd logs
 
 ### Chat History
 
-*   History is saved to files in `~/.local/share/gemini-cli/history/`.
-*   To maintain history *across separate `gemini` commands*, the `GEMINI_SESSION_ID` environment variable must be set (the wrapper function helps manage this).
-*   Use `--new-chat` to start fresh, `--disable-history` to temporarily ignore/not save history.
-*   Long conversations are automatically summarized to manage token limits.
+*   History is saved to files in `~/.local/share/gemini-suite/history/`.
+*   Requires the wrapper function (installed by the installer) to work correctly across shell sessions.
 
 ### Memory Features
 
-Powered by `gemini-memory` and LanceDB (`~/.local/share/gemini-cli/memory.db`).
+Powered by `gemini-memory` and LanceDB (`~/.local/share/gemini-suite/memory.db`).
 
 *   **Memory Broker (`--enable-memory-broker` / `--disable-memory-broker`):** Automatically retrieves relevant past memories and adds them as context to your prompts.
 *   **Auto Memory (`--enable-auto-memory` / `--disable-auto-memory`):** Automatically extracts and saves key information from conversations.

README.md

@@ -0,0 +1,55 @@
+# Plan for Unified Configuration in Gemini Suite
+
+**Goal:** Consolidate configuration loading logic and settings for all Gemini Suite components (CLI, daemons) into a single source of truth (`gemini-core/src/config.rs`), managed by the `core` crate and potentially generated/updated by the `tools/generate_unified_config.rs` script. Exclude `mcp_servers.json`.
+
+**Plan:**
+
+1.  **Define Unified Configuration Structure (`core` crate):**
+    *   Create `core/src/config.rs`.
+    *   Define `UnifiedConfig` struct holding all settings, using nested structs (e.g., `CliConfig`, `HappeConfig`, etc.).
+    *   Derive `serde::Serialize` and `serde::Deserialize`.
+    *   Choose TOML format and standard location (e.g., `~/.config/gemini-suite/config.toml` or env var `GEMINI_SUITE_CONFIG_PATH`).
+
+2.  **Implement Configuration Loading (`core` crate):**
+    *   Add dependencies (`serde`, `toml`, `config-rs`/`figment`, `directories`) to `core/Cargo.toml`.
+    *   Implement `load_config()` in `core/src/config.rs` to:
+        *   Find config file path.
+        *   Read and deserialize into `UnifiedConfig`.
+        *   Handle errors.
+        *   (Optional) Merge sources (file, env vars).
+
+3.  **Audit and Refactor Crates:**
+    *   **For each relevant crate (`cli`, `daemon-manager`, `happe`, `ida`, `mcp`, `memory`):**
+        *   **3.1 Audit:** Systematically search the crate's codebase (using `grep`, IDE search, etc.) for *any* existing configuration mechanisms:
+            *   Reading environment variables (e.g., `std::env::var`).
+            *   Reading specific config files (e.g., `.env`, custom formats).
+            *   Hardcoded configuration values.
+            *   `clap` arguments used for configuration values (not just operational flags).
+            *   Any pre-existing attempts at unified configuration.
+            *   **Maintain a meticulous log (`UNIFIED_CONFIG_REFACTOR_LOG.md`)** detailing the file, line number, and type of configuration found in each crate *before* refactoring.
+        *   **3.2 Add Dependency:** Add `gemini-core` to the crate's `Cargo.toml`.
+        *   **3.3 Refactor:** In the crate's entry point/initialization:
+            *   Call `gemini_core::config::load_config()` once.
+            *   Remove *all* identified legacy configuration logic (from step 3.1).
+            *   Pass the relevant parts of the loaded `UnifiedConfig` struct (e.g., `config.happe`) to the components needing them. Update function signatures and struct definitions as necessary.
+            *   **Update the refactoring log** indicating the changes made to replace the legacy logic with the unified config approach.
+    *   **Note:** Handle `install` and `tools` crates appropriately (config generation vs. runtime needs). `ipc` likely needs no config.
+
+4.  **Update Configuration Generator (`tools/generate_unified_config.rs`):**
+    *   Add `gemini-core` dependency.
+    *   Modify script to:
+        *   Use `gemini_core::config::UnifiedConfig`.
+        *   Populate defaults.
+        *   Serialize to TOML.
+        *   Write to the standard config path.
+
+5.  **Update Documentation:**
+    *   Modify `README.md` files (root, `cli`, `daemon-manager`, `happe`, `ida`, `mcp`, `memory`).
+    *   Document unified config file (location, format, structure, modification).
+    *   Explain `generate_unified_config` tool's role.
+
+6.  **Testing:**
+    *   Unit tests for `core::config::load_config()`.
+    *   Integration tests for all components verifying config usage.
+    *   Test overriding defaults.
+    *   Run `cargo clippy --all -- -D warnings` and `cargo fmt --all`.