feat(cli): add Cortex CLI agent-native development tool (#1)

Complete implementation of the Cortex CLI including:
- TUI framework with reactive components and terminal rendering
- Multi-provider AI integration (Anthropic, OpenAI, Groq, Google, etc.)
- MCP (Model Context Protocol) client and server support
- Plugin architecture for extensibility
- Session management and persistence
- File operations and shell execution tools
- LSP integration for code intelligence
- Background task execution system
- Network proxy capabilities
- Comprehensive agent system with custom agent support

Technical highlights:
- Rust workspace with modular crate architecture
- Cross-platform support (Linux, macOS, Windows)
- GitHub Actions CI/CD workflows
- Multi-distribution publishing (Homebrew, Winget, R2)

Author: echobt

.cargo/audit.toml

@@ -0,0 +1,13 @@
+# audit.toml - cargo-audit configuration for security audit
+# https://github.com/rustsec/rustsec/blob/main/cargo-audit/audit.toml.example
+#
+# This file consolidates all RUSTSEC advisory exceptions in one place.
+# These are known vulnerabilities in transitive dependencies that cannot be
+# easily upgraded, typically due to deep dependency chains (e.g., wasmtime).
+
+[advisories]
+# No longer needed - wasmtime updated to v41, ratatui to v0.30
+ignore = []
+
+# Warn on informational advisories (unmaintained, unsound, etc.)
+informational_warnings = ["unmaintained", "unsound", "notice"]

.cargo/config.toml

@@ -0,0 +1,42 @@
+# Cargo configuration for static linking with musl targets
+# This enables building portable, statically-linked Linux binaries
+
+# =============================================================================
+# x86_64 musl target (static linking)
+# =============================================================================
+[target.x86_64-unknown-linux-musl]
+# Use the musl-cross toolchain linker for cross-compilation
+# If building on a musl-based system, this can be simplified to just "musl-gcc"
+rustflags = [
+    "-C", "target-feature=+crt-static",
+    "-C", "link-self-contained=yes"
+]
+
+# =============================================================================
+# aarch64 musl target (static linking)
+# =============================================================================
+[target.aarch64-unknown-linux-musl]
+rustflags = [
+    "-C", "target-feature=+crt-static",
+    "-C", "link-self-contained=yes"
+]
+
+# =============================================================================
+# Build configuration
+# =============================================================================
+[build]
+# Use nightly for multithreaded compilation (set via RUSTFLAGS in CI)
+# rustflags = ["-Zthreads=32"]
+
+# =============================================================================
+# Net configuration (for faster crate downloads)
+# =============================================================================
+[net]
+retry = 3
+git-fetch-with-cli = true
+
+# =============================================================================
+# Registry configuration (sparse protocol for faster index updates)
+# =============================================================================
+[registries.crates-io]
+protocol = "sparse"

.github/hooks/pre-commit

@@ -0,0 +1,42 @@
+#!/bin/sh
+# Pre-commit hook for Cortex CLI (OPTIMIZED)
+# Only formats and checks CHANGED Rust files
+
+set -e
+
+echo "=== Pre-commit Hook (Optimized) ==="
+
+# Get list of staged Rust files
+STAGED_RS_FILES=$(git diff --cached --name-only --diff-filter=ACMR | grep '\.rs$' || true)
+
+if [ -z "$STAGED_RS_FILES" ]; then
+    echo "No Rust files staged, skipping checks."
+    exit 0
+fi
+
+echo "Checking $(echo "$STAGED_RS_FILES" | wc -l | tr -d ' ') Rust file(s)..."
+
+# Format only staged files with rustfmt directly (faster than cargo fmt)
+echo "Running rustfmt on staged files..."
+echo "$STAGED_RS_FILES" | xargs rustfmt --edition 2024 2>/dev/null || true
+
+# Re-add formatted files
+echo "$STAGED_RS_FILES" | xargs git add
+
+# Quick clippy on changed crates only (find unique crate directories)
+CHANGED_CRATES=$(echo "$STAGED_RS_FILES" | sed 's|/src/.*||' | sort -u | grep -v '^\.' || true)
+
+if [ -n "$CHANGED_CRATES" ]; then
+    echo "Running clippy --fix on changed crates..."
+    for crate in $CHANGED_CRATES; do
+        if [ -f "$crate/Cargo.toml" ]; then
+            crate_name=$(basename "$crate")
+            cargo clippy -p "$crate_name" --fix --allow-dirty --allow-staged 2>/dev/null || true
+        fi
+    done
+    
+    # Re-add any clippy fixes
+    echo "$STAGED_RS_FILES" | xargs git add 2>/dev/null || true
+fi
+
+echo "=== Pre-commit passed! ==="

.github/hooks/pre-push

@@ -0,0 +1,79 @@
+#!/bin/sh
+# Pre-push hook for Cortex CLI (OPTIMIZED)
+# Only checks crates with changes since origin
+
+set -e
+
+echo "=== Pre-push Hook (Optimized) ==="
+
+# Get the remote branch we're pushing to
+REMOTE=${1:-origin}
+REMOTE_REF=$(git rev-parse --abbrev-ref @{upstream} 2>/dev/null || echo "$REMOTE/master")
+
+# Get changed Rust files since remote
+CHANGED_RS_FILES=$(git diff --name-only "$REMOTE_REF"...HEAD | grep '\.rs$' || true)
+
+if [ -z "$CHANGED_RS_FILES" ]; then
+    echo "No Rust files changed since $REMOTE_REF, skipping checks."
+    exit 0
+fi
+
+echo "Checking changes since $REMOTE_REF..."
+
+# Find changed crates
+CHANGED_CRATES=$(echo "$CHANGED_RS_FILES" | sed 's|/src/.*||' | sort -u | grep -v '^\.' || true)
+
+# Format check on changed files only
+echo "Running rustfmt --check on changed files..."
+echo "$CHANGED_RS_FILES" | xargs rustfmt --edition 2024 --check 2>/dev/null || {
+    echo "ERROR: Format check failed. Run 'cargo fmt' to fix."
+    exit 1
+}
+
+# Clippy only on changed crates
+if [ -n "$CHANGED_CRATES" ]; then
+    echo "Running clippy on changed crates..."
+    CLIPPY_ARGS=""
+    for crate in $CHANGED_CRATES; do
+        if [ -f "$crate/Cargo.toml" ]; then
+            crate_name=$(basename "$crate")
+            # Skip cortex-gui (needs frontend built)
+            if [ "$crate_name" != "cortex-gui" ] && [ "$crate_name" != "src-tauri" ]; then
+                CLIPPY_ARGS="$CLIPPY_ARGS -p $crate_name"
+            fi
+        fi
+    done
+    
+    if [ -n "$CLIPPY_ARGS" ]; then
+        cargo clippy $CLIPPY_ARGS --lib 2>&1 | head -50 || true
+    fi
+fi
+
+# Check only changed crates
+echo "Running cargo check on changed crates..."
+for crate in $CHANGED_CRATES; do
+    if [ -f "$crate/Cargo.toml" ]; then
+        crate_name=$(basename "$crate")
+        if [ "$crate_name" != "cortex-gui" ] && [ "$crate_name" != "src-tauri" ]; then
+            cargo check -p "$crate_name" 2>/dev/null || {
+                echo "ERROR: cargo check failed for $crate_name"
+                exit 1
+            }
+        fi
+    fi
+done
+
+# Run tests only on changed crates
+echo "Running tests on changed crates..."
+for crate in $CHANGED_CRATES; do
+    if [ -f "$crate/Cargo.toml" ]; then
+        crate_name=$(basename "$crate")
+        if [ "$crate_name" != "cortex-gui" ] && [ "$crate_name" != "src-tauri" ]; then
+            cargo test -p "$crate_name" --lib 2>/dev/null || {
+                echo "WARNING: Tests failed for $crate_name (continuing)"
+            }
+        fi
+    fi
+done
+
+echo "=== Pre-push passed! ==="