more milestone work

AGENTS.md

@@ -23,14 +23,14 @@ When writing or modifying code:
 2. When module-level invariants are apparent, write an `@liyi:module` block — in the directory's existing module doc (`README.md`, `doc.go`, `mod.rs` doc comment, etc.) or in a dedicated `LIYI.md`. Use the doc markup language's comment syntax for the marker.
 3. If a source item has a `@liyi:related <name>` annotation, record the dependency in `.liyi.jsonc` as `"related": {"<name>": null}`. The tool fills in the requirement's current hash.
 4. For each `@liyi:requirement <name>` block encountered, ensure it has a corresponding entry in the co-located `.liyi.jsonc` with `"requirement"` and `"source_span"`. (The tool fills in `"source_hash"`.)
-5. If a spec has `"related"` edges referencing a requirement, do not overwrite the requirement text during inference. Re-anchor the spec (update `source_span`) but preserve the `"related"` edges. Do not write `source_hash` — the tool fills it in.
+5. If a spec has `"related"` edges referencing a requirement, do not overwrite the requirement text during inference. Update the spec (update `source_span`) but preserve the `"related"` edges. Do not write `source_hash` — the tool fills it in.
 6. Only generate adversarial tests from items that have a `@liyi:intent` annotation in source or `"reviewed": true` in the sidecar (i.e., human-reviewed intent). When `@liyi:intent` is present in source, use its prose (or the docstring for `=doc`) as the authoritative intent for test generation.
 7. Tests should target boundary conditions, error-handling gaps, property violations, and semantic mismatches. Prioritize tests a subtly wrong implementation would fail.
 8. Skip items annotated with `@liyi:ignore` or `@liyi:trivial`, and files matched by `.liyiignore`. Respect `@liyi:nontrivial` — if present, always infer a spec for that item and never override with `@liyi:trivial`.
 9. Use a different model for test generation than the one that wrote the code, when possible.
 10. When `liyi check` reports stale items, choose one of two paths:
     - **Direct re-inference** (preferred during interactive editing with few stale items): re-read the source, update `source_span` and `intent` in the sidecar, leave `"reviewed"` unset. Appropriate when you are the agent that just made the change, the number of stale items is small, and the changes are straightforward.
-    - **Triage** (preferred for batch workflows, CI, or when many items are stale): assess each item — is the change cosmetic, semantic, or an intent violation? Write the assessment to `.liyi/triage.json` following the triage report schema. For cosmetic changes, run `liyi triage --apply` to auto-reanchor. For semantic changes, propose updated intent in `suggested_intent`. For intent violations, flag for human review. Prefer triage when stale items have `"reviewed": true` or `@liyi:intent` in source — these carry human-vouched intent that deserves explicit assessment, not silent re-inference.
+    - **Triage** (preferred for batch workflows, CI, or when many items are stale): assess each item — is the change cosmetic, semantic, or an intent violation? Write the assessment to `.liyi/triage.json` following the triage report schema. For cosmetic changes, run `liyi triage --apply` to auto-fix. For semantic changes, propose updated intent in `suggested_intent`. For intent violations, flag for human review. Prefer triage when stale items have `"reviewed": true` or `@liyi:intent` in source — these carry human-vouched intent that deserves explicit assessment, not silent re-inference.
 11. Before committing, run `liyi check`. If it reports coverage gaps (missing requirement specs, missing related edges), resolve **all** gaps in the same commit. Do not commit with unresolved coverage gaps — CI will reject it.
 
 ### `.liyi.jsonc` Schema (v0.1)
@@ -104,7 +104,7 @@ Sidecar files must conform to the following JSON Schema. The top-level object ha
         },
         "source_hash": {
           "$ref": "#/$defs/sourceHash",
-          "description": "Tool-managed. SHA-256 hex digest of the source lines in the span. Computed by liyi reanchor or the linter — agents should not produce this."
+          "description": "Tool-managed. SHA-256 hex digest of the source lines in the span. Computed by liyi check --fix — agents should not produce this."
         },
         "source_anchor": {
           "type": "string",
@@ -128,7 +128,7 @@ Sidecar files must conform to the following JSON Schema. The top-level object ha
         },
         "_hints": {
           "type": "object",
-          "description": "Transient inference aids emitted by liyi init for cold-start scenarios. LLM-readable, intentionally unstructured. Stripped by liyi reanchor after initial review. Tools MUST NOT rely on any specific shape."
+          "description": "Transient inference aids emitted by liyi init for cold-start scenarios. LLM-readable, intentionally unstructured. Stripped by liyi check --fix after initial review. Tools MUST NOT rely on any specific shape."
         }
       }
     },
@@ -149,7 +149,7 @@ Sidecar files must conform to the following JSON Schema. The top-level object ha
         },
         "source_hash": {
           "$ref": "#/$defs/sourceHash",
-          "description": "Tool-managed. Computed by liyi reanchor or the linter."
+          "description": "Tool-managed. Computed by liyi check --fix."
         },
         "source_anchor": {
           "type": "string",
@@ -215,8 +215,8 @@ When `liyi check` reports stale items, the agent assesses each and writes the re
     },
     "action": {
       "type": "string",
-      "enum": ["auto-reanchor", "update-intent", "fix-code-or-update-intent", "manual-review"],
-      "description": "Recommended action. auto-reanchor for cosmetic, update-intent for semantic, fix-code-or-update-intent for intent-violation, manual-review for unclear."
+      "enum": ["auto-fix", "update-intent", "fix-code-or-update-intent", "manual-review"],
+      "description": "Recommended action. auto-fix for cosmetic, update-intent for semantic, fix-code-or-update-intent for intent-violation, manual-review for unclear."
     },
     "summary": {
       "type": "object",

README.md

@@ -30,8 +30,8 @@ liyi check --root .
 ## How It Works
 
 1. **Agent infers intent** — today's agents automatically read `AGENTS.md`, which teaches them the 立意 pattern. During normal development they maintain `.liyi.jsonc` sidecar files for each code item, with `source_span` and natural-language `intent`. If they don't do it automatically, you can always tell them to.
-2. **`liyi check`** — hashes source spans, detects staleness and shifts, checks review status, tracks requirement edges. Zero network, zero LLM, fully deterministic.
-3. **`liyi reanchor`** — re-hashes spans after intentional code changes. Never modifies intent or review state.
+2. **`liyi check`** — hashes source spans, detects staleness and shifts, checks review status, tracks requirement edges. Zero network, zero LLM, fully deterministic. With `--fix`, auto-corrects shifted spans, fills missing hashes, and computes `tree_path`.
+3. **`liyi migrate`** — upgrades sidecar files when the schema version changes. Idempotent.
 4. **Human reviews** — sets `"reviewed": true` in the sidecar to approve, or adds `@liyi:intent` in source to provide the authoritative human version.
 
 ## Progressive Adoption
@@ -55,10 +55,8 @@ liyi check [OPTIONS] [PATHS]...
     --fail-on-req-changed <true|false> Fail on changed requirements (default: true)
     --root <PATH>                   Override repo root
 
-liyi reanchor [FILE]
-    --item <NAME>     Target a specific item
-    --span <S,E>      Override span (1-indexed, inclusive)
-    --migrate         Schema version migration
+liyi migrate [FILE|DIR]...
+    Upgrade sidecar schema version
 ```
 
 ## Exit Codes

README.zh.md

@@ -31,8 +31,8 @@ liyi check --root .
 ## 工作原理
 
 1. **由智能体推断意图** — 当今的智能体会自动读取 `AGENTS.md`，于是便掌握了《立意》设计模式。在正常开发流程中，它们便会自动为每个代码条目维护 `.liyi.jsonc` sidecar 文件，包含 `source_span` 和自然语言 `intent`。如果没有自动维护，也总可以明确告诉它这么干。
-2. **`liyi check`** — 为智能体提供的源码区间计算内容哈希，检测内容是否过时、行号是否偏移、是否被复核过，并追踪需求边。零网络访问、零 LLM 依赖、行为完全确定。
-3. **`liyi reanchor`** — 在有意的代码变更后重新计算区间哈希。不修改意图或复核状态。
+2. **`liyi check`** — 为智能体提供的源码区间计算内容哈希，检测内容是否过时、行号是否偏移、是否被复核过，并追踪需求边。零网络访问、零 LLM 依赖、行为完全确定。加 `--fix` 可自动修正偏移区间、填充缺失哈希、计算 `tree_path`。
+3. **`liyi migrate`** — 当 schema 版本变更时升级 sidecar 文件。幂等。
 4. **由人类复核** — 在 `.liyi.jsonc` 中设置 `"reviewed": true` 以批准，或在源码中添加 `@liyi:intent` 以明确给出人类版本。
 
 ## 渐进式采用
@@ -56,10 +56,8 @@ liyi check [OPTIONS] [PATHS]...
     --fail-on-req-changed <true|false> 对已变更需求报错（默认：true）
     --root <PATH>                   覆盖仓库根目录
 
-liyi reanchor [FILE]
-    --item <NAME>     指定目标条目
-    --span <S,E>      覆盖区间（1 起始，闭区间）
-    --migrate         执行 schema 版本迁移
+liyi migrate [FILE|DIR]...
+    升级 sidecar schema 版本
 ```
 
 ## 退出状态码

crates/liyi-cli/src/cli.rs

@@ -68,23 +68,10 @@ pub enum Commands {
         level: DiagnosticLevel,
     },
 
-    /// Re-hash source spans in sidecar files
-    Reanchor {
-        /// Sidecar files or directories to reanchor (recursive)
-        #[arg(required_unless_present = "migrate")]
+    /// Migrate sidecar files to the current schema version
+    Migrate {
+        /// Sidecar files or directories to migrate (recursive)
         files: Vec<PathBuf>,
-
-        /// Target a specific item by name
-        #[arg(long, requires = "span")]
-        item: Option<String>,
-
-        /// Override span (start,end)
-        #[arg(long, requires = "item", value_parser = parse_span)]
-        span: Option<[usize; 2]>,
-
-        /// Migrate sidecar to current schema version
-        #[arg(long)]
-        migrate: bool,
     },
 
     /// Scaffold AGENTS.md or skeleton .liyi.jsonc sidecar
@@ -116,20 +103,3 @@ pub enum Commands {
         item: Option<String>,
     },
 }
-
-/// Parse a "start,end" string into a [usize; 2] span.
-fn parse_span(s: &str) -> Result<[usize; 2], String> {
-    let parts: Vec<&str> = s.split(',').collect();
-    if parts.len() != 2 {
-        return Err(format!("expected format 'start,end', got '{s}'"));
-    }
-    let start: usize = parts[0]
-        .trim()
-        .parse()
-        .map_err(|_| format!("invalid start: '{}'", parts[0].trim()))?;
-    let end: usize = parts[1]
-        .trim()
-        .parse()
-        .map_err(|_| format!("invalid end: '{}'", parts[1].trim()))?;
-    Ok([start, end])
-}

crates/liyi-cli/src/cli.rs.liyi.jsonc

@@ -30,26 +30,14 @@
     {
       "item": "Commands",
       "reviewed": false,
-      "intent": "Enumerate all CLI subcommands (Check, Reanchor, Init, Approve) with their full set of flags and arguments, providing defaults and mutual constraints (e.g. --item requires --span, file is required unless --migrate, --level filters diagnostic output).",
+      "intent": "Enumerate all CLI subcommands (Check, Migrate, Init, Approve) with their full set of flags and arguments, providing defaults and mutual constraints (e.g. --level filters diagnostic output).",
       "source_span": [
         28,
-        118
+        105
       ],
       "tree_path": "enum::Commands",
-      "source_hash": "sha256:383b23d5dbade566788d2673cb55fc05e8e7e33b70f4e2edd77df0245d09db65",
+      "source_hash": "sha256:94096c9cb7d64c3fd721c783da0c3f0482f6b548e317daac6b2c1d0ec902dd63",
       "source_anchor": "pub enum Commands {"
-    },
-    {
-      "item": "parse_span",
-      "reviewed": true,
-      "intent": "Parse a 'start,end' string into a [usize; 2] span, rejecting inputs that are not exactly two comma-separated unsigned integers.",
-      "source_span": [
-        121,
-        135
-      ],
-      "tree_path": "fn::parse_span",
-      "source_hash": "sha256:d57d01b6fb8d7fbefc54c62e3240b46d80cc2370a7d148811caad6d809b23977",
-      "source_anchor": "fn parse_span(s: &str) -> Result<[usize; 2], String> {"
     }
   ]
 }

crates/liyi-cli/src/main.rs

@@ -89,23 +89,13 @@ fn main() {
 
             process::exit(exit_code as i32);
         }
-        Commands::Reanchor {
-            files,
-            item,
-            span,
-            migrate,
-        } => {
-            if migrate && files.is_empty() {
-                eprintln!("--migrate requires at least one sidecar file path");
-                process::exit(2);
-            }
-
+        Commands::Migrate { files } => {
             if files.is_empty() {
                 eprintln!("at least one sidecar file or directory required");
                 process::exit(2);
             }
 
-            let targets = match liyi::reanchor::resolve_reanchor_targets(&files) {
+            let targets = match liyi::discovery::resolve_sidecar_targets(&files) {
                 Ok(t) => t,
                 Err(e) => {
                     eprintln!("Error: {e}");
@@ -120,13 +110,9 @@ fn main() {
 
             let mut errors = 0;
             for sidecar_path in &targets {
-                match liyi::reanchor::run_reanchor(sidecar_path, item.as_deref(), span, migrate) {
+                match liyi::reanchor::run_reanchor(sidecar_path, None, None, true) {
                     Ok(()) => {
-                        if migrate {
-                            println!("Migrated: {}", sidecar_path.display());
-                        } else {
-                            println!("Reanchored: {}", sidecar_path.display());
-                        }
+                        println!("Migrated: {}", sidecar_path.display());
                     }
                     Err(e) => {
                         eprintln!("Error ({}): {e}", sidecar_path.display());

crates/liyi-cli/src/main.rs.liyi.jsonc

@@ -21,19 +21,19 @@
       "intent": "=doc",
       "source_span": [
         26,
-        242
+        228
       ],
       "tree_path": "fn::main",
-      "source_hash": "sha256:a11828b49d8e7c5b144423442c9bab41b1d84aff99c551e159e0c03558f70b06",
+      "source_hash": "sha256:5c447be7165dcba8bfd3d08fff588db7b2d95309ec9c474aa30487deeec02d49",
       "source_anchor": "fn main() {"
     },
     {
       "item": "is_tty",
       "reviewed": true,
       "intent": "=doc",
       "source_span": [
-        248,
-        250
+        234,
+        236
       ],
       "tree_path": "fn::is_tty",
       "source_hash": "sha256:36dcd447c8fa9e666c6682395c3148c216b7c07dce8cc88f3d76f90714207ccd",

crates/liyi/Cargo.toml

@@ -30,6 +30,10 @@ tree-sitter-php = "0.24.2"
 tree-sitter-objc = "3.0.2"
 tree-sitter-kotlin-ng = "1.1.0"
 tree-sitter-swift = "0.7.1"
+tree-sitter-bash = "0.25.1"
+tree-sitter-ruby = "0.23.1"
+tree-sitter-zig = "1.1.2"
+nom = "8"
 
 [dev-dependencies]
 proptest = "1"

crates/liyi/src/approve.rs

@@ -2,8 +2,8 @@ use std::fs;
 use std::io;
 use std::path::{Path, PathBuf};
 
+use crate::discovery::resolve_sidecar_targets;
 use crate::hashing::hash_span;
-use crate::reanchor::resolve_reanchor_targets;
 use crate::sidecar::{Spec, parse_sidecar, write_sidecar};
 
 /// Result of an approve operation on a single sidecar.
@@ -75,7 +75,7 @@ pub fn collect_approval_candidates(
     paths: &[PathBuf],
     item_filter: Option<&str>,
 ) -> Result<Vec<ApprovalCandidate>, ApproveError> {
-    let targets = resolve_reanchor_targets(paths).map_err(ApproveError::Parse)?;
+    let targets = resolve_sidecar_targets(paths).map_err(ApproveError::Parse)?;
     if targets.is_empty() {
         return Err(ApproveError::NoTargets);
     }

crates/liyi/src/approve.rs.liyi.jsonc

@@ -60,13 +60,13 @@
         130
       ],
       "tree_path": "fn::collect_approval_candidates",
-      "source_hash": "sha256:1fc98ea41edd3bed9c13d936635399d5e27a81f1f8acec326368b1eb532bda7c",
+      "source_hash": "sha256:f16f381eb67bf6126a0acfe022aac1ee575696b1d32a5cb46cee6bf2eb15a1d2",
       "source_anchor": "pub fn collect_approval_candidates("
     },
     {
       "item": "apply_approval_decisions",
       "reviewed": false,
-      "intent": "Apply a parallel slice of Decision values to the candidates, grouped by sidecar file. For Yes: set reviewed=true and reanchor hashes. For No: set reviewed=false. For Skip: no mutation. Write back modified sidecars unless dry_run. Returns per-sidecar ApproveResult.",
+      "intent": "Apply a parallel slice of Decision values to the candidates, grouped by sidecar file. For Yes: set reviewed=true and fill hashes. For No: set reviewed=false. For Skip: no mutation. Write back modified sidecars unless dry_run. Returns per-sidecar ApproveResult.",
       "source_span": [
         137,
         206