feat: global --source-root — index/mv/check/fix one subtree; deterministic Java FQN resolution in monorepos with duplicate packages (guava vs android/guava); move mv_reject to output.rs

docs/EXAMPLES.md

@@ -4,9 +4,9 @@ Concrete examples for both audiences: humans at a terminal and AI agents
 consuming `--json`. All outputs below are captured from the real binary.
 
 Flags (see `jmove --help`): `mv <source> <target> [--dry-run] [--json]
-[--no-git]`, `check [--json]`, and the global `--root <DIR>`. Paths may be
+[--no-git]`, `check [--json]`, and the global `--root <DIR>` /
-relative to the root or absolute inside it; `.gitignore`d files are never
+`--source-root <DIR>` (index one subtree only — the monorepo disambiguator
-indexed. Inside a git repo, `mv` of a tracked file uses `git mv` (the
+for duplicate Java packages). `.gitignore`d files are never indexed. Inside a git repo, `mv` of a tracked file uses `git mv` (the
 rename is staged); `--no-git` forces a plain filesystem rename.
 Exit codes: `0` ok · `1` operation error · `2` `check` found broken imports.
 

docs/SKILL.md

@@ -18,7 +18,7 @@ kept in sync); Python/Go on the roadmap. Single binary, no LSP needed.
 ### mv — move a file and rewrite its importers
 
 ```
-jmove mv <source> <target> [--root DIR] [--dry-run] [--json] [--no-git]
+jmove mv <source> <target> [--root DIR] [--source-root DIR] [--dry-run] [--json] [--no-git]
 ```
 
 Always run `--dry-run` first and confirm the change set looks right.
@@ -80,6 +80,12 @@ without `--dry-run`. For Java projects the practical loop is: `mv` →
 - `check` never reports unresolved Java imports (jdk, third-party,
   `pkg.*`) as broken — they are external by design, like TS bare
   specifiers.
+- Monorepos with duplicate packages (`guava` vs `android/guava` under one
+  `--root`): the same FQN exists in parallel trees, so resolution picks the
+  sorted-first copy and a move rewrites the wrong files. Pass the global
+  `--source-root DIR` to index (and fix/move) only that subtree; each tree
+  is then self-contained and correct. Without the flag behavior is
+  unchanged; `--source-root` on a non-directory exits 1.
 
 ## Recommended agent workflow
 

src/cli/fix.rs

@@ -71,12 +71,20 @@ pub struct FixDryRunData {
 }
 
 /// `fix` handler: validate rule, index, plan, then dry-run or apply.
-pub fn fix(root: &Path, rule: Option<&str>, dry_run: bool, json: bool) -> Flow<i32> {
+pub fn fix(
+    root: &Path,
+    source_root: Option<&Path>,
+    rule: Option<&str>,
+    dry_run: bool,
+    json: bool,
+) -> Flow<i32> {
     let root = flow(json, "fix", root.canonicalize().map_err(JmoveError::from))?;
+    let source_root = flow(json, "fix", super::normalize_scope(&root, source_root))?;
     if let Some(rejected) = fix_reject(rule) {
         return Err(fail(json, "fix", rejected));
     }
-    let index = flow(json, "fix", Index::build(&root))?;
+    let scope = source_root.as_deref();
+    let index = flow(json, "fix", Index::build_scoped(&root, scope))?;
     let plan = plan_fix(&index, rule);
     if plan.is_empty() {
         if json {

src/cli/mod.rs

@@ -29,6 +29,10 @@ pub struct Args {
     /// Project root (defaults to the current directory).
     #[arg(long, global = true, default_value = ".")]
     pub root: PathBuf,
+    /// Index only files under this root-relative directory: the monorepo
+    /// disambiguator for duplicate Java packages (`guava` vs `android/guava`).
+    #[arg(long, global = true)]
+    pub source_root: Option<PathBuf>,
 }
 
 /// Available subcommands (MVP: `mv`, `check`).
@@ -95,13 +99,27 @@ pub fn run() -> anyhow::Result<i32> {
             dry_run,
             json,
             no_git,
-        } => mv(&args.root, &source, &target, dry_run, json, no_git),
+        } => mv(
-        Command::Check { json } => check(&args.root, json),
+            &args.root,
+            args.source_root.as_deref(),
+            &source,
+            &target,
+            dry_run,
+            json,
+            no_git,
+        ),
+        Command::Check { json } => check(&args.root, args.source_root.as_deref(), json),
         Command::Fix {
             rule,
             dry_run,
             json,
-        } => fix::fix(&args.root, rule.as_deref(), dry_run, json),
+        } => fix::fix(
+            &args.root,
+            args.source_root.as_deref(),
+            rule.as_deref(),
+            dry_run,
+            json,
+        ),
     };
     // Handlers report their own failures; both arms carry an exit code.
     Ok(outcome.unwrap_or_else(identity))
@@ -110,6 +128,7 @@ pub fn run() -> anyhow::Result<i32> {
 /// `mv` handler: normalize paths, validate, index, plan, then dry-run or apply.
 fn mv(
     root: &Path,
+    source_root: Option<&Path>,
     source: &Path,
     target: &Path,
     dry_run: bool,
@@ -118,13 +137,15 @@ fn mv(
 ) -> Flow<i32> {
     let git = apply::GitMode::from_no_git(no_git);
     let root = flow(json, "mv", root.canonicalize().map_err(JmoveError::from))?;
+    let source_root = flow(json, "mv", normalize_scope(&root, source_root))?;
     let source = flow(json, "mv", core::rel_from_root(&root, source))?;
     let target = flow(json, "mv", core::rel_from_root(&root, target))?;
-    if let Some(rejected) = mv_reject(&root, &source, &target) {
+    if let Some(rejected) = output::mv_reject(&root, &source, &target) {
         return Err(fail(json, "mv", rejected));
     }
 
-    let index = flow(json, "mv", Index::build(&root))?;
+    let scope = source_root.as_deref();
+    let index = flow(json, "mv", Index::build_scoped(&root, scope))?;
     let plan = flow(json, "mv", plan::plan_move(&index, &source, &target))?;
     if dry_run {
         return mv_dry_run(&root, json, &plan, git);
@@ -149,48 +170,6 @@ fn mv(
     Ok(exit::OK)
 }
 
-/// Pre-flight `mv` validation. A file that exists on disk but is absent
-/// from the import index stays moveable: its plan simply has no rewrites.
-fn mv_reject(root: &Path, source: &Path, target: &Path) -> Option<ErrorData> {
-    let bad = |code: &str, message: String, hint: &str| {
-        Some(ErrorData::new(code, message, Some(hint.into())))
-    };
-    if source == target {
-        let msg = "source and target are the same path".into();
-        return bad("INVALID_ARGUMENT", msg, "pick a different destination");
-    }
-    if !root.join(source).is_file() {
-        let msg = format!("source file '{}' does not exist", core::rel_str(source));
-        return bad(
-            "SOURCE_NOT_FOUND",
-            msg,
-            "check the path or run `jmove check`",
-        );
-    }
-    if root.join(target).exists() {
-        let msg = format!("target path '{}' already exists", core::rel_str(target));
-        return bad(
-            "TARGET_EXISTS",
-            msg,
-            "remove or rename the existing target first",
-        );
-    }
-    // `target` names a file, so `parent()` always yields the directory part.
-    let parent = root.join(target.parent().unwrap_or(Path::new("")));
-    if parent.exists() && !parent.is_dir() {
-        let msg = format!(
-            "target parent of '{}' is not a directory",
-            core::rel_str(target)
-        );
-        return bad(
-            "INVALID_ARGUMENT",
-            msg,
-            "pick a destination inside a directory",
-        );
-    }
-    None
-}
-
 /// Dry-run branch: unified diff for humans, structured preview for agents.
 fn mv_dry_run(root: &Path, json: bool, plan: &MovePlan, git: apply::GitMode) -> Flow<i32> {
     let diff = flow(json, "mv", apply::render_diff(root, plan))?;
@@ -211,9 +190,11 @@ fn mv_dry_run(root: &Path, json: bool, plan: &MovePlan, git: apply::GitMode) ->
 /// Exit code is `2` when at least one broken import was found, in both the
 /// human and the `--json` mode (the JSON `status` stays `"ok"` — the
 /// command itself succeeded; agents read `total` or the exit code).
-fn check(root: &Path, json: bool) -> Flow<i32> {
+fn check(root: &Path, source_root: Option<&Path>, json: bool) -> Flow<i32> {
     let root = flow(json, "check", root.canonicalize().map_err(JmoveError::from))?;
-    let index = flow(json, "check", Index::build(&root))?;
+    let source_root = flow(json, "check", normalize_scope(&root, source_root))?;
+    let scope = source_root.as_deref();
+    let index = flow(json, "check", Index::build_scoped(&root, scope))?;
     let broken = flow(json, "check", output::broken_imports(&root, &index))?;
     let code = if broken.is_empty() {
         exit::OK
@@ -234,6 +215,21 @@ fn check(root: &Path, json: bool) -> Flow<i32> {
     Ok(code)
 }
 
+/// Validate the global `--source-root`: project-relative, existing dir.
+fn normalize_scope(root: &Path, scope: Option<&Path>) -> JmoveResult<Option<PathBuf>> {
+    let Some(scope) = scope else {
+        return Ok(None);
+    };
+    let rel = core::rel_from_root(root, scope)?;
+    if !root.join(&rel).is_dir() {
+        return Err(JmoveError::InvalidArgument(format!(
+            "--source-root '{}' is not a directory",
+            core::rel_str(&rel)
+        )));
+    }
+    Ok(Some(rel))
+}
+
 /// Unwrap a core result, routing failures through the CLI error channel.
 fn flow<T>(json: bool, operation: &'static str, result: JmoveResult<T>) -> Flow<T> {
     result.map_err(|err| fail(json, operation, ErrorData::from_core(&err)))

src/cli/output.rs

@@ -11,7 +11,7 @@ use crate::core::index::Index;
 use crate::core::plan::{MovePlan, Rewrite};
 use crate::core::{JmoveResult, rel_str};
 
-use super::json::{BrokenImport, Change, ChangedFile};
+use super::json::{BrokenImport, Change, ChangedFile, ErrorData};
 
 /// `check` stdout line when the project has no broken imports.
 const CHECK_CLEAN: &str = "check: no broken imports found";
@@ -95,6 +95,47 @@ pub fn changed_files(root: &Path, plan: &MovePlan) -> JmoveResult<Vec<ChangedFil
         .collect())
 }
 
+/// Pre-flight `mv` validation: `(root, source, target)` are project-relative
+/// and normalized. A file that exists on disk but is absent from the import
+/// index stays moveable: its plan simply has no rewrites.
+#[must_use]
+pub fn mv_reject(root: &Path, source: &Path, target: &Path) -> Option<ErrorData> {
+    let bad = |code: &str, message: String, hint: &str| {
+        Some(ErrorData::new(code, message, Some(hint.into())))
+    };
+    if source == target {
+        let msg = "source and target are the same path".into();
+        return bad("INVALID_ARGUMENT", msg, "pick a different destination");
+    }
+    if !root.join(source).is_file() {
+        let msg = format!("source file '{}' does not exist", rel_str(source));
+        return bad(
+            "SOURCE_NOT_FOUND",
+            msg,
+            "check the path or run `jmove check`",
+        );
+    }
+    if root.join(target).exists() {
+        let msg = format!("target path '{}' already exists", rel_str(target));
+        return bad(
+            "TARGET_EXISTS",
+            msg,
+            "remove or rename the existing target first",
+        );
+    }
+    // `target` names a file, so `parent()` always yields the directory part.
+    let parent = root.join(target.parent().unwrap_or(Path::new("")));
+    if parent.exists() && !parent.is_dir() {
+        let msg = format!("target parent of '{}' is not a directory", rel_str(target));
+        return bad(
+            "INVALID_ARGUMENT",
+            msg,
+            "pick a destination inside a directory",
+        );
+    }
+    None
+}
+
 /// `moved src -> tgt, updated N imports in M files` success summary,
 /// noting when the rename went through `git mv`.
 #[must_use]

src/core/index/mod.rs

@@ -54,6 +54,15 @@ impl Index {
     /// Scan `root`, parse every supported source file and build the graph.
     /// Unreadable or unparseable files are skipped, not fatal.
     pub fn build(root: &Path) -> JmoveResult<Self> {
+        Self::build_scoped(root, None)
+    }
+
+    /// Like [`build`](Self::build), but when `source_root` (project-relative,
+    /// normalized) is `Some`, only files under that subtree are indexed. This
+    /// is the monorepo escape hatch: `guava` vs `android/guava` declare the
+    /// same FQNs, and scoping the index to one self-contained copy makes
+    /// collision-free resolution (and therefore `mv`/`fix` rewrites) exact.
+    pub fn build_scoped(root: &Path, source_root: Option<&Path>) -> JmoveResult<Self> {
         let root = root.canonicalize()?;
         let mut index = Self {
             root,
@@ -62,7 +71,7 @@ impl Index {
             packages: HashMap::new(),
             java_classes: JavaClassIndex::default(),
         };
-        index.scan()?;
+        index.scan(source_root)?;
         // Resolution needs the complete file set (extension/index guessing)
         // and the full package map, so it runs as a second pass.
         let java_classes = JavaClassIndex::new(&index.files, &index.packages);
@@ -83,11 +92,17 @@ impl Index {
     }
 
     // Walk the project and parse each supported source file, staging the
-    // raw records with `target: None` for the resolution pass above.
+    // raw records with `target: None` for the resolution pass above. When
-    fn scan(&mut self) -> JmoveResult<()> {
+    // `source_root` (project-relative, normalized) is set, only files under
-        // Sorted map: deterministic discovery order.
+    // that subtree are indexed — see [`Index::build_scoped`].
+    fn scan(&mut self, source_root: Option<&Path>) -> JmoveResult<()> {
+        // Sorted map: deterministic discovery order. Walking starts at the
+        // scoped subtree when set, so the rest of the monorepo is not even
+        // opened; paths stay root-relative because the prefix removed is
+        // always `self.root`.
         let mut found: BTreeMap<PathBuf, SourceLanguage> = BTreeMap::new();
-        for entry in WalkBuilder::new(&self.root).require_git(false).build() {
+        let base = source_root.map_or(self.root.clone(), |scope| self.root.join(scope));
+        for entry in WalkBuilder::new(base).require_git(false).build() {
             // Walker errors (unreadable dirs, etc.) simply skip the entry.
             let Ok(entry) = entry else { continue };
             if entry.path_is_symlink() || !entry.file_type().is_some_and(|t| t.is_file()) {

src/core/index/tests.rs

@@ -119,3 +119,81 @@ fn importers_of_returns_sorted_reverse_edges() -> JmoveResult<()> {
     assert!(index.importers_of(Path::new("missing.ts")).is_empty());
     Ok(())
 }
+
+// The guava monorepo shape: `android/guava` and `guava` both declare
+// `com.example.App`, so an unscoped index resolves every importer to the
+// same (sorted-first) copy and a move in one tree rewrites the wrong files.
+fn monorepo() -> JmoveResult<tempfile::TempDir> {
+    let dir = tempfile::TempDir::new()?;
+    let root = dir.path();
+    for tree in ["guava", "android/guava"] {
+        write_file(
+            root,
+            &format!("{tree}/src/com/example/App.java"),
+            "package com.example;\npublic class App {}\n",
+        )?;
+        write_file(
+            root,
+            &format!("{tree}/src/com/example/Use.java"),
+            "package com.example;\nimport com.example.App;\nclass Use { App a; }\n",
+        )?;
+    }
+    Ok(dir)
+}
+
+fn resolved_target(index: &Index, importer: &str) -> Option<PathBuf> {
+    index
+        .imports
+        .get(Path::new(importer))?
+        .iter()
+        .find_map(|r| r.target.clone())
+}
+
+#[test]
+fn unscoped_index_resolves_the_duplicate_fqn_to_the_sorted_first_tree() -> JmoveResult<()> {
+    let dir = monorepo()?;
+    let index = Index::build(dir.path())?;
+    // Both trees' `App` collide; the class index keeps `android/guava` (sorts first).
+    assert_eq!(
+        resolved_target(&index, "guava/src/com/example/Use.java").as_deref(),
+        Some(Path::new("android/guava/src/com/example/App.java")),
+        "demonstrates the collision the flag exists to fix"
+    );
+    Ok(())
+}
+
+#[test]
+fn source_root_scopes_indexing_so_the_fqn_resolves_within_the_tree() -> JmoveResult<()> {
+    let dir = monorepo()?;
+    let index = Index::build_scoped(dir.path(), Some(Path::new("guava")))?;
+    // Only the guava tree is indexed at all.
+    assert!(
+        index
+            .files
+            .contains(Path::new("guava/src/com/example/App.java"))
+    );
+    assert!(
+        !index
+            .files
+            .contains(Path::new("android/guava/src/com/example/App.java"))
+    );
+    assert_eq!(
+        resolved_target(&index, "guava/src/com/example/Use.java").as_deref(),
+        Some(Path::new("guava/src/com/example/App.java")),
+        "the scoped index resolves to the same tree"
+    );
+    Ok(())
+}
+
+#[test]
+fn source_root_does_not_leak_siblings_sharing_a_name_prefix() -> JmoveResult<()> {
+    // `--source-root guava` must match the directory `guava`, not `guavaX`.
+    let dir = tempfile::TempDir::new()?;
+    let root = dir.path();
+    write_file(root, "guava/src/A.java", "package p;\npublic class A {}\n")?;
+    write_file(root, "guavax/src/B.java", "package p;\npublic class B {}\n")?;
+    let index = Index::build_scoped(root, Some(Path::new("guava")))?;
+    assert!(index.files.contains(Path::new("guava/src/A.java")));
+    assert!(!index.files.contains(Path::new("guavax/src/B.java")));
+    Ok(())
+}

tests/cli_java.rs

@@ -149,3 +149,56 @@ fn default_package_file_cannot_change_directory() {
     .success();
     assert!(in_root(tmp.path(), "src/main/java/Run.java").is_file());
 }
+
+fn monorepo() -> tempfile::TempDir {
+    fixture("monorepo")
+}
+
+#[test]
+fn source_root_scopes_the_move_to_one_duplicate_tree() {
+    let tmp = monorepo();
+    jmove(
+        &tmp,
+        &[
+            "mv",
+            "--source-root",
+            "guava",
+            "guava/src/com/example/Primitives.java",
+            "guava/src/com/example/util/Primitives.java",
+        ],
+    )
+    .success()
+    .stdout(predicate::str::contains("updated 2 imports in 2 files"));
+
+    // The scoped tree moved and its importer followed the new package.
+    let app = read(&in_root(tmp.path(), "guava/src/com/example/app/App.java"));
+    assert!(app.contains("import com.example.util.Primitives;"), "{app}");
+    let moved = read(&in_root(
+        tmp.path(),
+        "guava/src/com/example/util/Primitives.java",
+    ));
+    assert!(moved.contains("package com.example.util;"), "{moved}");
+
+    // The sibling copy is a self-contained tree: not one byte touched.
+    let android = read(&in_root(
+        tmp.path(),
+        "android/guava/src/com/example/app/App.java",
+    ));
+    assert!(
+        android.contains("import com.example.Primitives;"),
+        "{android}"
+    );
+    assert!(in_root(tmp.path(), "android/guava/src/com/example/Primitives.java").is_file());
+    jmove(&tmp, &["check", "--source-root", "guava"]).success();
+}
+
+#[test]
+fn unknown_source_root_is_rejected() {
+    let tmp = monorepo();
+    jmove(&tmp, &["check", "--source-root", "nope"])
+        .failure()
+        .code(1)
+        .stderr(predicate::str::contains(
+            "--source-root 'nope' is not a directory",
+        ));
+}

tests/java/monorepo/android/guava/src/com/example/Primitives.java

@@ -0,0 +1,3 @@
+package com.example;
+
+public class Primitives {}

tests/java/monorepo/android/guava/src/com/example/app/App.java

@@ -0,0 +1,5 @@
+package com.example.app;
+
+import com.example.Primitives;
+
+public class App { Primitives p; }

tests/java/monorepo/guava/src/com/example/Primitives.java

@@ -0,0 +1,3 @@
+package com.example;
+
+public class Primitives {}

tests/java/monorepo/guava/src/com/example/app/App.java

@@ -0,0 +1,5 @@
+package com.example.app;
+
+import com.example.Primitives;
+
+public class App { Primitives p; }

todo.md

@@ -74,9 +74,10 @@ AI оставляем СНАРУЖИ: при неоднозначности jmov
 - [ ] (после fix) повторить обе перемещения как `mv` + авто-`fix` и добить compile до SUCCESS
       (паттерн воспроизведён и закрыт локально: mv файла с bare-ссылкой на соседний пакет →
       `fix` добавил импорт → javac SUCCESS; на реальном guava ещё не прогонялось)
-- [ ] Индексация в monorepo с дублями пакетов (guava vs android/guava в одном --root):
+- [x] Индексация в monorepo с дублями пакетов (guava vs android/guava в одном --root):
-      FQN-коллизии → class_index оставляет первый по сортировке, импорт резолвится не туда.
+      глобальный `--source-root DIR` — индексирует (mv/check/fix) только поддерево,
-      Нужен выбор/фильтр source root (например `--source-root` или авто-определение по mv-цели)
+      FQN-коллизии исчезают, соседнее дерево не трогается; авто-определение по mv-цели
+      осознанно НЕ делаем (явный флаг предсказуемее, см. KISS)
 
 ## Phase 2
 - [ ] Кэш индекса на диске (bincode/rkyv) → .jmove/index