docs: Add comprehensive timeout configuration documentation

[echobt]

Summary

This PR adds comprehensive documentation for timeout configuration across the Cortex codebase. It documents the timeout hierarchy, explains when each timeout applies, and provides guidance on which constants to use for consistency.

Changes

• Add detailed timeout hierarchy documentation in cortex-common/http_client.rs
• Document all timeout constants with their purpose and recommended usage
• Add inline comments referencing standard timeout values in config files
• Include a table showing which timeout applies to each use case

Timeout Hierarchy

Use Case	Module	Constant	Value	Rationale
Health checks	cortex-common/http_client	HEALTH_CHECK_TIMEOUT	5s	Quick validation
Standard HTTP requests	cortex-common/http_client	DEFAULT_TIMEOUT	30s	Normal API calls
Connection pool idle	cortex-common/http_client	POOL_IDLE_TIMEOUT	60s	DNS refresh
LLM Request (non-streaming)	cortex-exec/runner	DEFAULT_REQUEST_TIMEOUT_SECS	120s	Model inference
LLM Streaming total	cortex-common/http_client	STREAMING_TIMEOUT	300s	Long-running streams
Server request lifecycle	cortex-app-server/config	request_timeout	300s	Full request handling
Per-chunk reads	cortex-app-server/config	read_timeout	30s	Chunk timeout
Graceful shutdown	cortex-app-server/config	shutdown_timeout	30s	Time for cleanup
Entire execution	cortex-exec/runner	DEFAULT_TIMEOUT_SECS	600s	Headless exec limit

Verification

cargo check -p cortex-common
cargo doc -p cortex-common --no-deps

[greptile-apps]

Greptile Overview

Greptile Summary

This PR adds comprehensive documentation for timeout configuration across the Cortex codebase. The changes are purely documentation-focused with some dead code cleanup.

Documentation additions:

• Added extensive timeout hierarchy table in cortex-common/src/http_client.rs covering all timeout constants across the system (5s to 600s)
• Added cross-references from timeout-related fields in cortex-app-server/config.rs and cortex-exec/runner.rs pointing to the central documentation
• Provided clear guidance on when to use each timeout constant and recommendations for adding new timeouts

Code cleanup (unrelated to docs):

• Removed unused base_dir field from SessionStorage in storage.rs
• Removed unused replace_all field and with_replace_all method from SearchReplace in hunk.rs
• Removed unused reconnect and test_connection methods from transport.rs
• Cleaned up unused imports (sleep, error from tracing)

The documentation follows a clear hierarchy from shortest (health checks: 5s) to longest (full exec session: 600s), with proper rationale for each timeout value.

Confidence Score: 5/5

• This PR is safe to merge with no risk
• The changes are purely additive documentation with verified dead code removal. No logic changes, no behavioral modifications. The documentation accurately reflects the existing timeout constants in the codebase, and the dead code removal was verified to have no callers.
• No files require special attention

Important Files Changed

Filename	Overview
src/cortex-common/src/http_client.rs	Added comprehensive timeout hierarchy documentation as module-level doc comments
src/cortex-exec/src/runner.rs	Enhanced timeout constant documentation with cross-references to central docs
src/cortex-app-server/src/config.rs	Added cross-references to timeout hierarchy documentation in config fields

Sequence Diagram

sequenceDiagram
    participant User
    participant Server as cortex-app-server<br/>(request_timeout: 300s)
    participant Runner as cortex-exec<br/>(session timeout: 600s)
    participant HTTPClient as cortex-common<br/>http_client
    participant LLM as LLM API

    Note over User,LLM: Timeout Hierarchy in Action

    User->>Server: HTTP Request
    activate Server
    Note right of Server: request_timeout: 300s<br/>Full lifecycle limit

    Server->>Runner: Execute Task
    activate Runner
    Note right of Runner: DEFAULT_TIMEOUT_SECS: 600s<br/>Multi-turn session limit

    Runner->>HTTPClient: create_streaming_client()
    Note right of HTTPClient: STREAMING_TIMEOUT: 300s

    Runner->>LLM: LLM Request (via HTTPClient)
    activate LLM
    Note right of Runner: DEFAULT_REQUEST_TIMEOUT_SECS: 120s<br/>Single request timeout

    LLM-->>Runner: Streaming Response
    Note right of Server: read_timeout: 30s<br/>Per-chunk timeout
    deactivate LLM

    Runner-->>Server: Result
    deactivate Runner

    Server-->>User: HTTP Response
    deactivate Server

    Note over User,LLM: Health Check Flow (Fast Path)
    User->>HTTPClient: Health Check
    activate HTTPClient
    Note right of HTTPClient: HEALTH_CHECK_TIMEOUT: 5s<br/>Quick validation
    HTTPClient-->>User: Health Status
    deactivate HTTPClient

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[greptile-apps]

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[echobt]

Closing to consolidate: This timeout documentation will be merged with PR #86 into a consolidated documentation PR for timeout configuration.