- Added raw read output propagation so read/archive commands bypass anchors, line numbers, and chunk formatting.
- Fixed atom/hashline editing by tightening hashline prefixes and applying grouped anchor edits in stable order.
- Hardened chunk parsing and path handling by using `bigram_end` checks and resolving edit paths via shared `args.path` fallback.
- Updated path-related behavior for chunk, replace, patch, and hashline previews to honor optional edit paths.
- Removed mode-level param validators and replaced them with runtime handling, then removed obsolete validation tests.
- Added `atom` edit mode to `EditTool` with single-point hashline-style dispatch and `executeAtomSingle`.
- Added `AtomToolEdit`/`AtomParams` schema and `atom` prompt docs to require one op per edit entry.
- Changed `EditTool` entry processing to inherit per-entry `path` from a top-level request `path` fallback.
- Added top-level `path` defaults to patch and replace schemas and now reject missing entry paths.
- Added an `atom` streaming strategy and registered it in `EDIT_MODE_STRATEGIES` for live mode support.
- Enabled hashline read anchors for `atom` mode via `file-display-mode.ts` path-display logic.
- Added `atom` unit tests covering schema checks, anchor conflicts, and hash mismatch diagnostics.
- Aligned hashline and chunk token handling to `HASHLINE_BIGRAMS` in `computeLineHash` and parsing regexes.
- Removed hashline file-level `move`/`delete` options from schemas and execution so edits are in-place updates only.
- Hardened hashline prefix parsing to reject non-bigram IDs, preventing false stripping of `#` comment lines.
- Updated `read()`/prompt wording so raw reads skip prefixes and examples now show anchors like `123#th`.
- Updated hashline chunk tests for new `HASHLINE_BIGRAMS` IDs and replaced stale hash constants.
The previous mismatch text ('1 line has changed since last read. Use
the updated LINE#ID references shown below.') reads like a successful
edit followed by an informational note. Providers whose tool-result
plumbing does not surface `isError: true` to the model (e.g. Qwen via
the OpenAI-completions shim, where mitmproxy traces show the model only
receives the content text) treat the response as a success and proceed
with stale state.
Reword the message to start with 'Edit rejected:' and explicitly state
'The edit was NOT applied' so the failure is unambiguous in plaintext.
The structural payload (>>> markers, updated LINE#IDs) is unchanged.
Fixes#742
Slots a new "apply_patch" variant alongside the existing edit modes
(replace, patch, hashline, chunk, vim). The mode accepts a single input
string containing a Codex *** Begin Patch / *** End Patch envelope,
parses it with a new lenient parser (heredoc-tolerant), and fans each
file-op out to the existing executePatchSingle so LSP writethrough,
plan-mode guards, fs-cache invalidation and diagnostics are shared
with the patch mode.
Exposes both tool shapes from the spec: the JSON function-tool variant
(§1.2, {input: string}) and the OpenAI custom-tool / Lark-grammar
"freeform" variant (§1.1, raw patch string). The edit tool advertises
a Lark grammar via customFormat and a wire name via customWireName;
openai-responses emits it as a grammar-constrained custom tool when a
model opts in with applyPatchToolType: "freeform" in models.json.
custom_tool_call / custom_tool_call_output are plumbed end-to-end
through the shared responses code (emission, streaming, history
replay), and the agent-loop dispatcher matches tool calls by either
name or customWireName so returned calls route correctly.
Also threads preview/diff rendering for apply_patch through the TUI
(tool-execution + edit renderer) so streaming patches show per-file
diffs like the other edit modes.
Default edit mode is unchanged (hashline); opt in via edit.mode or
PI_EDIT_VARIANT=apply_patch.
- Standardized missing-file read errors and now return `File not found: <path>` for absent edit targets.
- Centralized AI provider, usage, and OAuth helpers into shared modules to remove duplicated logic.
- Migrated OAuth/API-key login flows to shared factory helpers and removed inline prompt/token-exchange code.
- Reused shared tools and formatter utilities for discovery, stream tails, LSP batching, and source formatting.
- Consolidated repeated test helpers and fixtures into shared modules, replacing inline helper duplicates.
The hashline prefix stripping logic uses an "all-or-nothing" heuristic:
it only strips N#XX: anchors when every non-empty line carries one.
When the Read tool truncation notice (e.g. [Showing lines 1-300 of
332. Use sel=L301 to continue]) is present in content passed to the
Edit or Write tool, that marker line breaks the heuristic, causing ALL
anchors to be written to disk verbatim. On subsequent reads, those
persisted anchors get double-prefixed (1#NX:1#BQ:---), compounding
the corruption.
This can happen when the AI model pastes Read tool output (including
the truncation marker) back into an Edit/Write call. While this is
arguably a model-level issue, the toolchain should be resilient against
it rather than silently corrupting files.
Changes:
- Add READ_TRUNCATION_NOTICE_RE to detect Read tool truncation markers
- Update collectLinePrefixStats to exclude truncation marker lines from
the non-empty line count so they no longer break the stripping heuristic
- Add stripLeadingHashlinePrefixes helper for recursive stripping of
nested/double-prefixed anchors (handles already-corrupted content)
- Add filterTruncationNotices helper to remove truncation marker lines
- Update both stripNewLinePrefixes and stripHashlinePrefixes to filter
truncation markers and use recursive anchor stripping
- Add 5 new test cases covering truncation markers and nested anchors
- Added `vim` as a supported edit mode and resolved mode-specific active tool names.
- Migrated chunk-edit requests from legacy `op`/`content` to `path` plus `write`, `replace`, and `insert`.
- Replaced chunk-edit internals with `put`/`replace`/`delete` operations and ID-based selection.
- Updated chunk prompts/output docs to document ID-based selectors and `write: null` deletions.
- Switched chunk and grep render output to `@`/dash-style anchors and updated file-count behavior for multi-file edits.
- Updated multi-file result rendering with distinct file counting and pending-file progress indicator.
- Refreshed chunk-mode and chunk-tree tests for the new contract and anchor style.
- Added hierarchical chunk grep output grouped by directory, file, and chunk with aligned chunk anchors.
- Updated chunk rendering to show clipped head/tail context with explicit truncation and expand markers.
- Changed chunk edit and streaming validation to use chunkToolEditSchema-based checks for safe edit detection.
- Enhanced grep rendering to use structured ChunkedGrepMatch data with displayPath and chunk checksum metadata.
- Updated chunk-mode and core chunk tests to use abbreviated chunk selectors introduced by path truncation.
- Adjusted expected chunk-path and error-path strings for markdown, Rust, and TLA+ fixtures to match the new naming scheme.
- Updated SIXEL sanitization assertions to check for the new "visible columns omitted" truncation message.
fixed retained-kernel restart and owner cleanup edge cases during recovery and disposal
tracked async user_python hooks during disposal-sensitive execution paths and hardened startup warmup tracking
strengthened cleanup and kernel lifecycle regressions to remove deadlocks, false positives, and timing flakes
scoped retained-kernel ownership to agent sessions and cleaned it up on session disposal
cleaned up warmed python owners on session startup failure and rejected new direct and tool-based python starts during disposal, including async hook, preflight, and warmup races
- Added language-aware chunking for Svelte, Vue, Astro, and HTML script/style tags using `lang` aliases.
- Added markdown/html markup handling for fenced code and HTML blocks with detected injected languages.
- Added injected-subtree chunk infrastructure and build-time merge logic in `pi-natives/chunk`.
- Added tests for markdown and script-chunking embedded-language behavior in chunk-tree and chunk-mode suites.
- Refactored chunk rendering to compute prologue and body line counts separately via new `chunk_head_body_lines()` function.
- Updated ellipsis marker format from line count to line range selection syntax (e.g., 'to expand above/below').
- Modified `render()` method signature to accept `head_lines` and `body_lines` parameters for precise line count display.
- Simplified no-changes response in chunk edit mode to omit redundant text when content matches.
- Expanded chunk-edit documentation with compound statement examples and region suffix behavior for non-code formats.
- Simplified chunk region notation from @head/@body/@tail/@decl to ^/~ suffix format across all modules.
- Removed ChunkRegion::Tail and ChunkRegion::Decl enum variants and updated region matching logic accordingly.
- Added call-with-callback pattern detection via try_promote_call_with_callback() and trailing_callback_body() functions.
- Updated documentation and test fixtures to reflect new region selector syntax throughout codebase.
- Extracted `raceWithAbort()` utility to pi-utils package for reuse across projects.
- Replaced local `raceAbort()` implementation with imported `raceWithAbort()` from pi-utils.
- Refactored cleanup timer to use async iterator pattern with `timers.setInterval()` instead of callback-based `setInterval()`.
- Converted `#cleanupIdleSessions()` and `#disposeSession()` from async to synchronous methods with async cleanup loop delegated to `#runCleanupLoop()`.
- Migrated language classifiers from imperative methods to declarative semantic rule tables with ClassifierTables and StructuralOverrides.
- Extracted node shape analysis into dedicated shape module with field priority constants and helper functions for AST traversal.
- Added schema module with language-aware node metadata and thread-local language context management.
- Centralized environment variable parsing across codebase using $flag(), $envpos(), and isBunTestRuntime() utilities.
- Added PI_CHUNK_AUTOINDENT configuration to control indentation normalization in chunk read/edit operations.
- Enhanced system prompt with instruction priority, output contract, tool persistence, and completeness guidelines.
- Corrected markdown section spacing logic to preserve blank lines between inserted sections and following headings.
- Added markdown-aware spacing detection to handle FirstChild, LastChild, Before, and After insert positions correctly.
- Added two test cases validating blank line preservation in markdown After and Append operations.
- Reformatted doc comments in RenderParams and ReadRenderParams for line length compliance.
- Extracted chunk tree formatting logic into dedicated `format_selector_tree()` function for reuse across error handling.
- Refactored error messages to display chunk children as hierarchical tree structure with line numbers and signatures instead of comma-separated lists.
- Removed `format_chunk_ref()` helper and consolidated formatting logic into tree-based error hint generation.
- Updated test assertions to validate tree-formatted output with regex patterns matching branch symbols and structure.
- Fixed file not found error handling in auto-generated marker detection to gracefully return undefined instead of propagating errors.
- Made assertEditableFileContent function synchronous to simplify API and improve error handling consistency.
- Updated test assertions to match synchronous function behavior using toThrow instead of rejects patterns.
- Removed obsolete test case for doc comment preservation during replace operations.
- Renamed ChunkRegion::Inner variant to Body across Rust and TypeScript for clearer semantics.
- Renamed chunk edit tool parameter from target to sel and made op required instead of optional.
- Removed region aliases (prologue, epilogue, inner) and simplified region validation to accept only head, body, tail.
- Replaced db.exec() calls with db.run() for SQL execution in auth-storage, agent-storage, and history-storage.
- Enhanced chunk edit documentation with comprehensive examples, indentation rules, and CRC refresh guidance.
- Improved chunk statement merging logic to consolidate leaf statements into parent function bodies by default.
- Added Auto QA tool (`report_tool_issue`) for automated tracking of unexpected tool behavior with environment variable and setting support.
- Added Python tool environment warmup on first execution to ensure prelude helpers are available before use.
- Fixed Python prelude introspection to respect execution timeout and signal options, preventing hangs.
- Refactored prelude documentation caching and loading logic into reusable helper functions with test environment awareness.
- Enhanced kernel introspection with optional timeout and signal parameters for better execution control.
- Added system prompt guidance to encourage agents to report tool issues via Auto QA when available.
- Refactored chunk anchor format from bracket notation to marker-based syntax with +++ and --- delimiters.
- Renamed chunk edit regions from @container/@prologue/@body/@epilogue to @head/@inner/@tail for clearer semantics.
- Simplified line-number selector resolution to auto-convert line targets to chunk paths with checksum format.
- Removed PI_DEV debug addon loading logic; PI_DEV now only enables loader diagnostics without changing candidate filenames.
- Added full-name aliases for chunk kind patterns (decls, expr, fn, meth, mod, params, ret, stmts, var) alongside abbreviated forms.
- Refactored sanitize_node_kind() to return &str instead of String; adjusted identifier passing logic across AST modules.
- Refactored chunk tree initialization to use explicit prologue/epilogue byte boundaries instead of None values.
- Extracted chunk resolution logic to use split_selector_crc_and_region() helper for improved code reuse.
- Reorganized package.json exports across multiple modules (autoresearch, cli, dap, edit, modes) for better API surface clarity.
- Updated test expectations for Go receiver method rendering and chunk selector formats to match refactored output.
- Consolidated notebook conversion logic and removed unused _createErrorToolResult helper function.
- Improved leading trivia preservation in chunk edits by detecting and maintaining line prefix whitespace.
- Replaced all Bun.which() calls with $which() utility from @oh-my-pi/pi-utils across 22 files.
- Removed findBashOnPath() wrapper function from procmgr.ts, consolidating binary path resolution.
- Updated AGENTS.md documentation to reflect new $which() API usage pattern.
- Centralized binary detection logic through shared utility, reducing code duplication.
- Added region-based chunk targeting with @container, @prologue, @body, @epilogue selectors for precise edit operations.
- Simplified chunk edit operations from 6 variants to 5 (replace, before, after, prepend, append) with unified region parameter.
- Removed checksum requirement from insert operations; only replace operations require #CRC suffix in selector.
- Added canonical indentation normalization with normalize_indent parameter for consistent tab-based rendering across file types.
- Refactored chunk selector format from separate crc/anchor fields to unified selector#CRC@region syntax for mutations.
- Added UnsupportedRegion status to chunk read operations for explicit handling of region availability per chunk type.
- Reorganized edit tool from `patch/` to `edit/` directory with dedicated mode subdirectories (chunk, patch, hashline, replace).
- Replaced line-scoped edit operations with substring-based `find` parameter and added `replace_body` operation for preserving signatures.
- Added chunk focus modes (Expanded, Collapsed, Container) and focused rendering to display only touched chunks and adjacent siblings.
- Implemented notebook (ipynb) language support with virtual source conversion and cell-based chunk parsing.
- Enhanced chunk edit error messages with consistent checksum mismatch reporting and improved chunk selector auto-resolution.
- Extracted edit mode implementations into separate modules with improved helper functions and LSP integration for diagnostics.
- Added fully-qualified anchor paths in chunk read output showing complete path hierarchy with CRC checksums.
- Added exact chunk selector resolution with CRC validation to enforce canonical chunk paths in edit operations.
- Added `?` selector option to read syntax-aware chunks by canonical path listing when anchor paths are unclear.
- Improved tree-sitter range handling with `end_row_as_line()` function to correctly convert half-open ranges to 1-indexed line numbers.
- Extracted anchor label logic into `chunk_anchor_label()` const function and consolidated style-based selection.
- Removed --dev flag support from native build pipeline and dev:native npm scripts.
- Refactored chunk selector resolution to extract and preserve raw selector strings separately from parsed CRC checksums.
- Reorganized chunk state lookup infrastructure with dedicated maps for checksum, leaf, and suffix-based chunk resolution.
- Simplified batch operation CRC validation to auto-accept stale checksums for subsequent operations on the same chunk.
- Unified TypeScript interface and Nix attrset chunk classification with consistent naming and nested expression handling.
- Extracted clipboard utility functions to dedicated module with improved OSC 52 and Termux support.
- Updated chunk read formatting with anchorStyle parameter and ellipsis standardization for improved consistency.
- Migrated native bindings from TypeScript wrappers to NAPI-RS generated modules with auto-generated type definitions and runtime enums.
- Replaced chunk tree API with stateful ChunkState class supporting render, edit, and resolve operations with improved error handling.
- Converted callback signatures to error-first pattern (error, result) for shell, PTY, glob, and grep operations.
- Introduced type-safe enums for MacOSAppearance, GrepOutputMode, KeyEventType, ImageFormat, and AstMatchStrictness replacing string literals.
- Refactored chunk tree implementation with dedicated modules for edit, indent, resolve, and state management with comprehensive validation.
- Moved clipboard utilities from native bindings to coding-agent package with improved OSC 52 and Termux compatibility.
- Added `anchorStyle` setting ("full", "kind", "bare") to control anchor name verbosity in chunk output.
- Changed anchor tag delimiters from `` to `[…]` and gutter separator from `│` to `|`.
- Changed edit response to render only changed hunks with context instead of the full chunk tree.
- Fixed zero-width insert detection to derive target indent from neighboring lines instead of replaced range.
- Improved indent selection for body-level insertions by picking deeper indent between two neighbors.
- Updated error messages to clarify insert vs splice operations and line range validation.
- Modified assertChecksum() return type to handle cases with default CRC and no explicit selector.
- Distributed language-specific AST classification logic from defaults module to individual language modules for 15+ languages.
- Simplified defaults module to minimal catch-all fallbacks, removing 341 lines of match-based classification logic.
- Consolidated chunk edit operations by removing splice operation and unifying with line-scoped replace parameters.
- Simplified chunk rendering output format by reducing thresholds and changing line count display from 'lines' to 'ln' suffix.
- Removed PI_CHUNK_SPLICES environment variable and chunkSplicesEnabled conditional logic throughout codebase.
- Migrated test mocking from bun:test mock API to vitest spyOn pattern across 9 test files.
- Extracted mock setup logic into reusable helper functions with Symbol.dispose cleanup pattern.
- Replaced manual beforeEach/afterEach and try-finally blocks with TypeScript 5.2 using declarations.
- Removed 178 lines of boilerplate mock initialization and restoration code from test suite.
- Renamed hashline operation types for clarity: append->append_at, prepend->prepend_at, append_eof->append_file, prepend_bof->prepend_file.
- Updated all operation type references in patch implementation, tests, and documentation to reflect new naming convention.
- Restructured hashline tool documentation with hierarchical sections and simplified examples for improved clarity.
- Consolidated validation rules and added explicit warning about invalid anchors and operation/field combinations.
- Added autoresearch extension with autonomous experiment loop supporting init, run, and log experiment tools for metric-driven optimization.
- Added widget placement system enabling extensions to position UI components above or below the editor via ExtensionWidgetOptions.
- Added dashboard controller with interactive overlay for viewing experiment results, metrics, and progress with keyboard navigation.
- Removed auto-correction logic for off-by-one range edits in hashline editor to preserve user intent in patch operations.
- Added state reconstruction utilities to parse autoresearch.jsonl logs and rebuild experiment state across sessions.
- Added comprehensive type definitions and helper utilities for metric parsing, ASI validation, and process management.
- Changed bash interceptor configuration from boolean flags to customizable pattern-based rules array.
- Clarified hashline range replace semantics: end parameter is now strictly exclusive boundary.
- Fixed bash interceptor to apply built-in default rules when no custom patterns are configured.
- Updated hashline range validation and calculations to enforce exclusive end semantics throughout.
- Added auto-reconnect capability for MCP servers with SSE stream monitoring and exponential retry backoff.
- Added tool-level reconnect handling for retriable connection errors (ECONNREFUSED, ECONNRESET, 404/502/503).
- Added `/mcp reconnect <name>` command for manual MCP server recovery.
- Improved reconnect robustness by aborting retries when MCP configuration changes via epoch checking.
- Extended transport reconnect handling to all transport types (stdio, HTTP/SSE) with unified onClose logic.
- Added comprehensive test coverage for MCPManager reconnect behavior and tool-level abort propagation.
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