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fix: batch merge of bug fixes (PRs #255, #256, #257, #258, #260, #261, #262, #264, #265, #268)#360

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echobt merged 21 commits intomasterfrom
batch-merge-2-fixes-prs-255-268
Jan 27, 2026
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fix: batch merge of bug fixes (PRs #255, #256, #257, #258, #260, #261, #262, #264, #265, #268)#360
echobt merged 21 commits intomasterfrom
batch-merge-2-fixes-prs-255-268

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@echobt echobt commented Jan 27, 2026

Summary

This PR consolidates 10 bug fix PRs into master:

Merged PRs:

Testing

  • cargo check -p cortex-cli passes
  • cargo fmt applied

Bounty Bot and others added 21 commits January 27, 2026 14:06
- #2319: Add --no-cache flag to MCP debug command with checked_at timestamp
- #2320: Re-evaluate CORTEX_API_URL env var during config reload
- #2321: Add Retry-After: 60 header to 429 rate limit responses
- #2322: Auto-create parent directories for run --output flag
- #2323: Add --limit/--offset pagination to models list with stable sorting
- #2324: Add write location validation for Docker read-only containers
  - New validate_write_locations() and check_write_permissions() functions
  - Add --check-writable flag to 'cortex debug paths' command
- #2325: Show draft status in PR state display
- #2326: Add --no-stream flag to properly disable streaming output
- #2327: Update TUI capture dimensions on terminal resize
- #2328: Validate model names in agent create command

Closes #2319, #2320, #2321, #2322, #2323, #2324, #2325, #2326, #2327, #2328
…, 2198, 2199, 2201 [skip ci]

Fixes:
- #2174: Exit code 0 when response truncated - now exits with code 2 on truncation
- #2175: Conflicting temperature/top-p - warns when both are specified
- #2176: Unknown session fields dropped - uses serde flatten to preserve extra fields
- #2177: DNS cached indefinitely - adds pool_idle_timeout for DNS re-resolution
- #2179: Temperature validation floating-point - uses epsilon-based comparison
- #2196: UTF-8 streaming corruption - adds Utf8StreamBuffer for multi-byte handling
- #2197: --no-session with resume - validates flag incompatibility
- #2198: MCP reconnection fd leak - cleans up before reconnection attempts
- #2199: YAML anchor/alias failures - adds merge key resolution
- #2201: History navigation in tmux - improves bounds checking and docs
… #2214, #2215 [skip ci]

Fixes:
- #2202: Add progress indicators to cortex pr command for large PRs
- #2204: Add support for user-defined model aliases in config
- #2206: Fix token double-counting in cortex stats for tool calls
- #2208: Properly cancel in-flight MCP requests on timeout
- #2211: Detect and warn about network mount boundaries in config discovery
- #2213: Add configurable shutdown_timeout for graceful SIGTERM handling
- #2214: Add circular reference detection to session import
- #2215: Add clear_with_scrollback method to reset terminal scroll buffer

Not fixed (features don't exist in codebase):
- #2207: cortex sessions merge command doesn't exist
- #2212: agent create --template flag doesn't exist
…, 2506, 2507, 2509 [skip ci]

Fixes:
- #2497: Add --rate-limit flag to scrape command
- #2498: Add --max-tokens flag with pre-validation for token count
- #2499: Add Access-Control-Max-Age header to CORS configuration
- #2500: Handle empty model responses gracefully (not as errors)
- #2501: Add --sso flag for enterprise SSO login
- #2504: Add --token flag for direct token authentication
- #2505: Add --all flag for logout to clear all accounts
- #2506: Add config set/unset subcommands
- #2507: Add --remote flag to agent list
- #2509: Add --filter flag to agent list
…, 2493, 2495, 2496 [skip ci]

Fixes:
- #2485: Add --language filter to debug lsp command
- #2487: Add --install flag to debug ripgrep command
- #2488: Add --purge flag to uninstall command
- #2489: Add --pre flag to upgrade command
- #2490: Add user_friendly_message() for API key errors with guidance
- #2491: Auto-detect shell from $SHELL env for completion command
- #2492: Add --cors and --cors-origin flags to serve command
- #2493: Add --depth flag for recursive crawling to scrape command
- #2495: Add --links flag to scrape command for link extraction
- #2496: Add --retry flag to scrape command for failed requests
…, 2536, 2539, 2540 [skip ci]

Fixes:
- #2508: Add --top-k flag to cortex run and warn about parameter compatibility
- #2510: Add agent install subcommand for registry installation
- #2514: Improve shell completion with special character handling for bash/zsh
- #2531: Add pr --diff flag to show PR diff without checkout
- #2533: Add pr --comments flag to view PR comments
- #2534: Add pr --apply flag to view/apply AI suggestions
- #2535: Add acp --allow-tool flag for tool whitelisting
- #2536: Add acp --deny-tool flag for tool blacklisting
- #2539: Add github uninstall subcommand to remove workflow
- #2540: Add github update subcommand to update workflow
…, 2696, 2697, 2699 [skip ci]

Fixes:
- #2688: Handle missing UID in /etc/passwd (container environments)
  - Added get_user_info() that falls back to uid:<number> format
  - Added UID display in debug system output
- #2689: Add --max-tokens flag to run command
- #2690: Add --system flag for system prompt to run command
- #2691: Add --output flag (alias for --format) to run command
- #2693: Report container memory limit instead of host RAM
  - Added cgroup v1/v2 detection for container memory limits
  - Shows (container limit) indicator in debug system output
- #2694: Add global --trace flag for trace-level logging
- #2695: SIGTERM cleanup for lock files
  - Added signal-hook for SIGTERM handling on Unix
  - Cleanup lock files and temp files on graceful shutdown
- #2696: Add global --verbose/-v flag (alias for --log-level debug)
- #2697: Add global --color flag (auto/always/never)
- #2699: Add --schema flag for JSON schema validation to run command
…, 2406, 2407, 2410 [skip ci]

Fixes:
- #2396: Handle BrokenPipe during streaming to prevent UI corruption
- #2397: Add parallel_tools capability to model listings for tool support granularity
- #2398: Add active file modification detection warning in debug file command
- #2399: Stop API token consumption when output pipe closes (SIGPIPE handling)
- #2400: Show clear message when already on target version with channel info
- #2402: Sort agent list by display_name instead of filename
- #2403: Add trust_proxy config and X-Real-IP header support for reverse proxy setups
- #2406: Preserve argument quoting in MCP get command output for copy-paste
- #2407: Add truncation indicator when streaming response is interrupted by error
- #2410: Add warning about temperature=0 having inconsistent behavior across providers
…, 2684, 2685, 2686 [skip ci]

Fixes:
- #2616: Add plugin command for plugin management (list, install, remove, enable, disable, show)
- #2617: Add feedback command for user feedback (bug reports, good/bad results)
- #2668: Fix FIFO blocking in debug file command by detecting special file types before reading
- #2679: Add lock command for protecting sessions from deletion
- #2680: Handle file descriptor limit errors gracefully with helpful error messages
- #2681: Add --quiet flag to run command for silent output
- #2683: Add --dry-run flag to run command for previewing
- #2684: Add --no-progress flag to run command for CI/CD
- #2685: Add --no-cache flag to run command for fresh requests
- #2686: Add --retry flag to run command for automatic retries
…, 2481, 2482, 2486 [skip ci]

Fixes:
- #2469: Add read_timeout config for chunked transfer handling
- #2473: (deferred - complex validation change)
- #2475: Improve mDNS error messages for service discovery
- #2476: Add --install flag to completion command
- #2477: Add --yes flag to init command for non-interactive mode
- #2479: Handle non-TTY gracefully in init command
- #2480: Add --branch flag to pr command for custom branch names
- #2481: (deferred - requires architectural changes for streaming)
- #2482: Add submit_batched_review API for GitHub PR comments
- #2486: Add model resolution warnings for ambiguous partial matches
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