cleanup: remove dead code and unnecessary allow(dead_code) annotations

[echobt]

Summary

This PR cleans up #[allow(dead_code)] annotations in several modules. Dead code is either removed if truly unused, or the annotation is removed if the code is actually used.

Changes

• cortex-app-server/src/storage.rs: Removed unused base_dir field from SessionStorage struct (the field was stored but never read after initialization)
• cortex-mcp-client/src/transport.rs: Removed unused reconnect() methods from both StdioTransport and HttpTransport, along with the unused test_connection() method from HttpTransport. Also removed unused imports (tokio::time::sleep and tracing::error)
• cortex-apply-patch/src/hunk.rs: Removed unused replace_all field and with_replace_all() method from SearchReplace struct (internal struct not exposed in public API)

Verification

cargo check -p cortex-app-server -p cortex-mcp-client -p cortex-apply-patch
cargo test -p cortex-app-server -p cortex-mcp-client -p cortex-apply-patch

[greptile-apps]

Greptile Overview

Greptile Summary

This PR removes dead code and unnecessary #[allow(dead_code)] annotations across three modules, resulting in cleaner, more maintainable code without any functional changes.

Changes:

• storage.rs: removed base_dir field from SessionStorage that was stored during initialization but never accessed
• transport.rs: removed reconnect() methods from both StdioTransport and HttpTransport that were never called, along with unused test_connection() helper and related imports
• hunk.rs: removed replace_all field and with_replace_all() builder method from SearchReplace struct that were never utilized

All removed code was verified to be truly unused through codebase searches. The changes are purely cleanup with no impact on functionality.

Confidence Score: 5/5

• This PR is safe to merge with no risk - it only removes genuinely unused code
• All changes were verified as truly dead code through codebase searches. No methods or fields being removed are referenced anywhere. The PR description accurately documents the changes and includes verification commands. This is pure cleanup with zero functional impact.
• No files require special attention

Important Files Changed

Filename	Overview
src/cortex-app-server/src/storage.rs	Removed unused base_dir field from SessionStorage struct - field was only used during initialization and never read afterward
src/cortex-mcp-client/src/transport.rs	Removed unused reconnect() methods from both transport implementations, unused test_connection() method, and unused imports (tokio::time::sleep, tracing::error)
src/cortex-apply-patch/src/hunk.rs	Removed unused replace_all field and with_replace_all() method from internal SearchReplace struct - functionality was never implemented

Sequence Diagram

sequenceDiagram
    participant Dev as Developer
    participant Compiler as Rust Compiler
    participant Code as Codebase
    
    Dev->>Code: Remove #[allow(dead_code)] annotations
    Dev->>Code: Delete unused struct fields
    Dev->>Code: Delete unused methods
    Dev->>Code: Remove unused imports
    
    Dev->>Compiler: cargo check
    Compiler->>Code: Analyze all packages
    Compiler-->>Dev: ✓ No dead_code warnings
    
    Dev->>Compiler: cargo test
    Compiler->>Code: Run tests for modified packages
    Compiler-->>Dev: ✓ All tests pass

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[greptile-apps]

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[echobt]

Closing as part of PR consolidation. This dead code cleanup has been consolidated into PR #77 (consolidated code quality improvements). See #77 for the comprehensive refactoring changes.