mars-agents 0.0.5

pub mod apply;
pub mod diff;
pub mod filter;
pub mod mutation;
pub mod plan;
pub mod provider;
pub mod rewrite;
pub mod self_package;
pub mod target;
pub mod types;

use std::collections::HashSet;
use std::path::PathBuf;

use crate::config::{Config, EffectiveConfig, Settings};
use crate::error::MarsError;
use crate::resolve::ResolveOptions;
use crate::source::GlobalCache;
use crate::sync::apply::ApplyResult;
pub use crate::sync::apply::SyncOptions;
use crate::types::{MarsContext, SourceName};
use crate::validate::ValidationWarning;

// Re-export mutation types for public API compatibility.
pub use crate::sync::mutation::{
    ConfigMutation, DependencyUpsertChange, LinkMutation, apply_config_mutation, mutate_link_config,
};

/// Report from a completed sync operation.
#[derive(Debug)]
pub struct SyncReport {
    pub applied: ApplyResult,
    pub pruned: Vec<apply::ActionOutcome>,
    pub warnings: Vec<ValidationWarning>,
    pub dependency_changes: Vec<DependencyUpsertChange>,
    /// Whether this was a dry run (`--diff`). Affects output wording only.
    pub dry_run: bool,
}

impl SyncReport {
    /// Whether the sync produced any unresolved conflicts.
    pub fn has_conflicts(&self) -> bool {
        self.applied
            .outcomes
            .iter()
            .any(|o| matches!(o.action, apply::ActionTaken::Conflicted))
    }
}

/// What a CLI command requests from the sync pipeline.
#[derive(Debug, Clone)]
pub struct SyncRequest {
    /// How to resolve versions.
    pub resolution: ResolutionMode,
    /// Config mutation to apply under flock.
    pub mutation: Option<ConfigMutation>,
    /// Behavior flags.
    pub options: SyncOptions,
}

/// Resolution behavior for the resolver stage.
#[derive(Debug, Clone)]
pub enum ResolutionMode {
    /// Normal sync behavior.
    Normal,
    /// Upgrade behavior (maximize versions), optionally scoped to specific sources.
    Maximize { targets: HashSet<SourceName> },
}

/// Execute the unified sync pipeline.
pub fn execute(ctx: &MarsContext, request: &SyncRequest) -> Result<SyncReport, MarsError> {
    let project_root = &ctx.project_root;
    let managed_root = &ctx.managed_root;
    let mars_dir = project_root.join(".mars");

    validate_request(request)?;

    std::fs::create_dir_all(mars_dir.join("cache"))?;

    // Step 1: Acquire sync lock before any config reads/mutations.
    let lock_path = mars_dir.join("sync.lock");
    let _sync_lock = crate::fs::FileLock::acquire(&lock_path)?;

    // Step 2: Load config under lock (auto-init when mutating and missing).
    let mut config = match crate::config::load(project_root) {
        Ok(config) => config,
        Err(err) if mutation::is_config_not_found(&err) && request.mutation.is_some() => Config {
            settings: Settings::default(),
            ..Config::default()
        },
        Err(err) => return Err(err),
    };

    // Step 3: Apply config mutation.
    let has_mutation = request.mutation.is_some();
    let dependency_changes = if let Some(m) = &request.mutation {
        mutation::apply_mutation(&mut config, m)?
    } else {
        Vec::new()
    };

    // Step 4: Load/mutate local overrides under the same lock.
    let mut local = crate::config::load_local(project_root)?;
    if let Some(m) = &request.mutation {
        mutation::apply_local_mutation(&mut local, m);
    }

    // Step 4b: Build effective config.
    let effective = crate::config::merge_with_root(config.clone(), local.clone(), project_root)?;

    // Step 5: Validate upgrade targets exist.
    validate_targets(&request.resolution, &effective)?;

    // Step 6: Load existing lock file.
    let old_lock = crate::lock::load(project_root)?;

    // Step 7: Resolve dependency graph.
    let cache = GlobalCache::new()?;
    let source_provider = provider::RealSourceProvider {
        cache: &cache,
        project_root,
    };
    let resolve_options = to_resolve_options(&request.resolution, request.options.frozen);
    let graph = crate::resolve::resolve(
        &effective,
        &source_provider,
        Some(&old_lock),
        &resolve_options,
    )?;

    // Step 8: Build target state.
    let (mut target_state, renames) = target::build_with_collisions(&graph, &effective)?;

    // Step 9: Handle collisions + rewrite frontmatter refs.
    if !renames.is_empty() {
        let rewrite_warnings = target::rewrite_skill_refs(&mut target_state, &renames, &graph)?;
        for w in &rewrite_warnings {
            eprintln!("{w}");
        }
    }

    // Step 10: Validate skill references.
    let warnings = validate_skill_refs(managed_root, &target_state);

    // Step 11: Prevent managed installs from overwriting unmanaged files.
    let unmanaged_collisions =
        target::check_unmanaged_collisions(managed_root, &old_lock, &target_state);
    for collision in &unmanaged_collisions {
        eprintln!(
            "warning: source `{}` collides with unmanaged path `{}` — leaving existing content untouched",
            collision.source_name, collision.path
        );
        target_state.items.shift_remove(&collision.path);
    }

    // Step 12: Compute diff.
    let sync_diff = diff::compute(
        managed_root,
        &old_lock,
        &target_state,
        request.options.force,
    )?;

    // Step 13: Create plan.
    let cache_bases_dir = mars_dir.join("cache").join("bases");
    let mut sync_plan = plan::create(&sync_diff, &request.options, &cache_bases_dir);

    // Step 13b-13c: Inject local package symlinks and handle _self lifecycle.
    let skipped_self_dests = self_package::inject_self_items(
        config.package.is_some(),
        project_root,
        managed_root,
        &old_lock,
        &mut target_state,
        &mut sync_plan,
    )?;

    // Step 14: Frozen gate.
    if request.options.frozen {
        let has_changes = sync_plan.actions.iter().any(|a| {
            !matches!(
                a,
                plan::PlannedAction::Skip { .. } | plan::PlannedAction::KeepLocal { .. }
            )
        });
        if has_changes {
            return Err(MarsError::FrozenViolation {
                message: "lock file would change but --frozen is set".into(),
            });
        }
    }

    // Step 15: Persist config/local only after validation gate and before apply.
    if has_mutation && !request.options.dry_run {
        match &request.mutation {
            Some(ConfigMutation::SetOverride { .. } | ConfigMutation::ClearOverride { .. }) => {
                crate::config::save_local(project_root, &local)?;
            }
            Some(
                ConfigMutation::UpsertDependency { .. }
                | ConfigMutation::BatchUpsert(..)
                | ConfigMutation::RemoveDependency { .. }
                | ConfigMutation::SetRename { .. },
            ) => {
                crate::config::save(project_root, &config)?;
            }
            None => {}
        }
    }

    // Step 16: Apply plan.
    let applied = apply::execute(managed_root, &sync_plan, &request.options, &cache_bases_dir)?;
    let pruned = Vec::new();

    // Step 17: Write lock file.
    if !request.options.dry_run {
        let self_lock_items = if config.package.is_some() {
            let self_items = self_package::discover_local_items(project_root)?;
            let filtered: Vec<_> = self_items
                .into_iter()
                .filter(|item| !skipped_self_dests.contains(&item.dest_rel))
                .collect();
            self_package::build_self_lock_items(&filtered)?
        } else {
            Vec::new()
        };
        let self_items_for_lock =
            (!self_lock_items.is_empty()).then_some(self_lock_items.as_slice());
        let new_lock = crate::lock::build(&graph, &applied, &old_lock, self_items_for_lock)?;
        crate::lock::write(project_root, &new_lock)?;
    }

    Ok(SyncReport {
        applied,
        pruned,
        warnings,
        dependency_changes,
        dry_run: request.options.dry_run,
    })
}

fn validate_request(request: &SyncRequest) -> Result<(), MarsError> {
    if request.options.frozen && matches!(request.resolution, ResolutionMode::Maximize { .. }) {
        return Err(MarsError::InvalidRequest {
            message:
                "cannot use --frozen with upgrade (frozen locks versions; upgrade maximizes them)"
                    .to_string(),
        });
    }

    if request.options.frozen && request.mutation.is_some() {
        return Err(MarsError::InvalidRequest {
            message:
                "cannot modify config in --frozen mode (config change would require lock update)"
                    .to_string(),
        });
    }

    Ok(())
}

fn validate_targets(
    resolution: &ResolutionMode,
    effective: &EffectiveConfig,
) -> Result<(), MarsError> {
    if let ResolutionMode::Maximize { targets } = resolution {
        for name in targets {
            if !effective.dependencies.contains_key(name) {
                return Err(MarsError::Source {
                    source_name: name.to_string(),
                    message: format!("dependency `{name}` not found in mars.toml"),
                });
            }
        }
    }

    Ok(())
}

fn to_resolve_options(mode: &ResolutionMode, frozen: bool) -> ResolveOptions {
    match mode {
        ResolutionMode::Normal => ResolveOptions {
            frozen,
            ..ResolveOptions::default()
        },
        ResolutionMode::Maximize { targets } => ResolveOptions {
            maximize: true,
            upgrade_targets: targets.clone(),
            frozen,
        },
    }
}

/// Validate skill references: check that agents' `skills:` frontmatter entries
/// reference skills that exist in the target state.
fn validate_skill_refs(
    install_target: &std::path::Path,
    target: &target::TargetState,
) -> Vec<ValidationWarning> {
    use crate::lock::ItemKind;

    // Collect available skill names
    let available_skills: HashSet<String> = target
        .items
        .values()
        .filter(|item| item.id.kind == ItemKind::Skill)
        .map(|item| item.id.name.to_string())
        .collect();

    // Collect agents with their paths
    let agents: Vec<(String, PathBuf)> = target
        .items
        .values()
        .filter(|item| item.id.kind == ItemKind::Agent)
        .map(|item| {
            let disk_path = install_target.join(&item.dest_path);
            // If the file exists on disk, use that (may have local edits).
            // Otherwise, use the source path.
            let path = if disk_path.exists() {
                disk_path
            } else {
                item.source_path.clone()
            };
            (item.id.name.to_string(), path)
        })
        .collect();

    crate::validate::check_deps(&agents, &available_skills).unwrap_or_default()
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::config::*;
    use crate::lock::{ItemKind, LockFile};
    use crate::resolve::{ResolvedGraph, ResolvedNode};
    use indexmap::IndexMap;
    use std::fs;
    use tempfile::TempDir;

    /// Helper to set up a complete sync context with temp dirs.
    struct TestFixture {
        project_root: TempDir,
        managed_root: PathBuf,
        source_trees: Vec<TempDir>,
    }

    impl TestFixture {
        fn new() -> Self {
            let project_root = TempDir::new().unwrap();
            let managed_root = project_root.path().join(".agents");
            // Create .mars/cache directories
            fs::create_dir_all(project_root.path().join(".mars/cache/bases")).unwrap();
            TestFixture {
                project_root,
                managed_root,
                source_trees: Vec::new(),
            }
        }

        fn add_source(&mut self, agents: &[(&str, &str)], skills: &[(&str, &str)]) -> usize {
            let dir = TempDir::new().unwrap();
            if !agents.is_empty() {
                let agents_dir = dir.path().join("agents");
                fs::create_dir_all(&agents_dir).unwrap();
                for (name, content) in agents {
                    fs::write(agents_dir.join(name), content).unwrap();
                }
            }
            if !skills.is_empty() {
                let skills_dir = dir.path().join("skills");
                fs::create_dir_all(&skills_dir).unwrap();
                for (name, content) in skills {
                    let skill_dir = skills_dir.join(name);
                    fs::create_dir_all(&skill_dir).unwrap();
                    fs::write(skill_dir.join("SKILL.md"), content).unwrap();
                }
            }
            self.source_trees.push(dir);
            self.source_trees.len() - 1
        }

        fn project_root(&self) -> &std::path::Path {
            self.project_root.path()
        }

        fn managed_root(&self) -> &std::path::Path {
            &self.managed_root
        }

        fn tree_path(&self, idx: usize) -> PathBuf {
            self.source_trees[idx].path().to_path_buf()
        }
    }

    fn make_graph_config(
        fixture: &TestFixture,
        sources: Vec<(&str, usize, FilterMode)>,
    ) -> (ResolvedGraph, EffectiveConfig) {
        let mut nodes = IndexMap::new();
        let mut order = Vec::new();
        let mut config_dependencies = IndexMap::new();

        for (name, tree_idx, filter) in sources {
            let tree_path = fixture.tree_path(tree_idx);
            nodes.insert(
                name.into(),
                ResolvedNode {
                    source_name: name.into(),
                    source_id: crate::types::SourceId::Path {
                        canonical: tree_path.clone(),
                    },
                    resolved_ref: crate::source::ResolvedRef {
                        source_name: name.into(),
                        version: None,
                        version_tag: None,
                        commit: None,
                        tree_path: tree_path.clone(),
                    },
                    manifest: None,
                    deps: vec![],
                },
            );
            order.push(name.into());

            config_dependencies.insert(
                name.into(),
                EffectiveDependency {
                    name: name.into(),
                    id: crate::types::SourceId::Path {
                        canonical: tree_path.clone(),
                    },
                    spec: SourceSpec::Path(tree_path),
                    filter,
                    rename: crate::types::RenameMap::new(),
                    is_overridden: false,
                    original_git: None,
                },
            );
        }

        (
            ResolvedGraph {
                nodes,
                order,
                id_index: std::collections::HashMap::new(),
            },
            EffectiveConfig {
                dependencies: config_dependencies,
                settings: Settings::default(),
            },
        )
    }

    fn path_dependency_entry(path: &std::path::Path) -> DependencyEntry {
        DependencyEntry {
            url: None,
            path: Some(path.to_path_buf()),
            version: None,
            filter: FilterConfig::default(),
        }
    }

    #[test]
    fn validate_request_rejects_frozen_with_maximize() {
        let request = SyncRequest {
            resolution: ResolutionMode::Maximize {
                targets: HashSet::new(),
            },
            mutation: None,
            options: SyncOptions {
                force: false,
                dry_run: false,
                frozen: true,
            },
        };

        let err = validate_request(&request).unwrap_err();
        assert!(matches!(err, MarsError::InvalidRequest { .. }));
        assert!(err.to_string().contains("--frozen"));
    }

    #[test]
    fn validate_request_rejects_frozen_with_mutation() {
        let request = SyncRequest {
            resolution: ResolutionMode::Normal,
            mutation: Some(ConfigMutation::RemoveDependency {
                name: "base".into(),
            }),
            options: SyncOptions {
                force: false,
                dry_run: false,
                frozen: true,
            },
        };

        let err = validate_request(&request).unwrap_err();
        assert!(matches!(err, MarsError::InvalidRequest { .. }));
        assert!(err.to_string().contains("cannot modify config"));
    }

    #[test]
    fn execute_auto_inits_config_for_mutation() {
        let project_root = TempDir::new().unwrap();
        let managed_root = project_root.path().join(".agents");
        fs::create_dir_all(project_root.path().join(".mars/cache/bases")).unwrap();
        let source = TempDir::new().unwrap();
        fs::create_dir_all(source.path().join("agents")).unwrap();
        fs::write(source.path().join("agents/coder.md"), "# Coder").unwrap();

        let request = SyncRequest {
            resolution: ResolutionMode::Normal,
            mutation: Some(ConfigMutation::UpsertDependency {
                name: "base".into(),
                entry: path_dependency_entry(source.path()),
            }),
            options: SyncOptions::default(),
        };

        let ctx = MarsContext::for_test(project_root.path().to_path_buf(), managed_root.clone());
        let report = execute(&ctx, &request).unwrap();
        assert!(!report.applied.outcomes.is_empty());
        assert!(project_root.path().join("mars.toml").exists());

        let saved = crate::config::load(project_root.path()).unwrap();
        assert!(saved.dependencies.contains_key("base"));
    }

    #[test]
    fn execute_dry_run_with_mutation_does_not_write_config() {
        let project_root = TempDir::new().unwrap();
        let managed_root = project_root.path().join(".agents");
        fs::create_dir_all(project_root.path().join(".mars/cache/bases")).unwrap();
        crate::config::save(
            project_root.path(),
            &Config {
                dependencies: IndexMap::new(),
                settings: Settings::default(),
                ..Config::default()
            },
        )
        .unwrap();

        let source = TempDir::new().unwrap();
        fs::create_dir_all(source.path().join("agents")).unwrap();
        fs::write(source.path().join("agents/coder.md"), "# Coder").unwrap();

        let request = SyncRequest {
            resolution: ResolutionMode::Normal,
            mutation: Some(ConfigMutation::UpsertDependency {
                name: "base".into(),
                entry: path_dependency_entry(source.path()),
            }),
            options: SyncOptions {
                force: false,
                dry_run: true,
                frozen: false,
            },
        };

        let ctx = MarsContext::for_test(project_root.path().to_path_buf(), managed_root.clone());
        let report = execute(&ctx, &request).unwrap();
        assert!(!report.applied.outcomes.is_empty());

        let saved = crate::config::load(project_root.path()).unwrap();
        assert!(!saved.dependencies.contains_key("base"));
        assert!(!managed_root.join("agents/coder.md").exists());
        assert!(!project_root.path().join("mars.lock").exists());
    }

    // === Integration tests for the pipeline stages ===

    #[test]
    fn full_pipeline_fresh_sync() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(
            &[("coder.md", "# Coder agent")],
            &[("planning", "# Planning skill")],
        );

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // Build target
        let (target, renames) = target::build_with_collisions(&graph, &config).unwrap();
        assert!(renames.is_empty());
        assert_eq!(target.items.len(), 2);

        // Compute diff against empty lock
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();

        // All items should be Add
        assert_eq!(sync_diff.items.len(), 2);
        for entry in &sync_diff.items {
            assert!(matches!(entry, diff::DiffEntry::Add { .. }));
        }

        // Create plan
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        assert_eq!(sync_plan.actions.len(), 2);
        for action in &sync_plan.actions {
            assert!(matches!(action, plan::PlannedAction::Install { .. }));
        }

        // Execute plan
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        assert_eq!(result.outcomes.len(), 2);

        // Verify files were created
        assert!(fixture.managed_root().join("agents/coder.md").exists());
        assert!(
            fixture
                .managed_root()
                .join("skills/planning/SKILL.md")
                .exists()
        );

        // Build lock
        let new_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();
        assert_eq!(new_lock.items.len(), 2);
        assert!(new_lock.items.contains_key("agents/coder.md"));
        assert!(new_lock.items.contains_key("skills/planning"));
    }

    #[test]
    fn re_sync_no_changes() {
        let mut fixture = TestFixture::new();
        let content = "# Coder agent";
        let src_idx = fixture.add_source(&[("coder.md", content)], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // First sync
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        let first_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();

        // Second sync with same content
        let (target2, _) = target::build_with_collisions(&graph, &config).unwrap();
        let sync_diff2 =
            diff::compute(fixture.managed_root(), &first_lock, &target2, false).unwrap();

        // All items should be Unchanged
        for entry in &sync_diff2.items {
            assert!(
                matches!(entry, diff::DiffEntry::Unchanged { .. }),
                "expected Unchanged, got {entry:?}"
            );
        }

        let sync_plan2 = plan::create(&sync_diff2, &options, &cache_dir);
        for action in &sync_plan2.actions {
            assert!(matches!(action, plan::PlannedAction::Skip { .. }));
        }
    }

    #[test]
    fn source_update_detects_changes() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[("coder.md", "# Version 1")], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // First sync
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        let first_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();

        // Update source content
        let agents_dir = fixture.tree_path(src_idx).join("agents");
        fs::write(agents_dir.join("coder.md"), "# Version 2").unwrap();

        // Rebuild target with updated content
        let (target2, _) = target::build_with_collisions(&graph, &config).unwrap();
        let sync_diff2 =
            diff::compute(fixture.managed_root(), &first_lock, &target2, false).unwrap();

        // Should detect an Update
        assert_eq!(sync_diff2.items.len(), 1);
        assert!(matches!(
            &sync_diff2.items[0],
            diff::DiffEntry::Update { .. }
        ));
    }

    #[test]
    fn local_modification_preserved() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[("coder.md", "# Original")], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // First sync
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        let first_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();

        // Locally modify the installed file
        fs::write(
            fixture.managed_root().join("agents/coder.md"),
            "# Locally modified",
        )
        .unwrap();

        // Re-sync (source unchanged)
        let (target2, _) = target::build_with_collisions(&graph, &config).unwrap();
        let sync_diff2 =
            diff::compute(fixture.managed_root(), &first_lock, &target2, false).unwrap();

        // Should detect LocalModified
        assert_eq!(sync_diff2.items.len(), 1);
        assert!(matches!(
            &sync_diff2.items[0],
            diff::DiffEntry::LocalModified { .. }
        ));

        // Plan should KeepLocal
        let sync_plan2 = plan::create(&sync_diff2, &options, &cache_dir);
        assert!(matches!(
            &sync_plan2.actions[0],
            plan::PlannedAction::KeepLocal { .. }
        ));
    }

    #[test]
    fn force_overwrites_local_modifications() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[("coder.md", "# Original")], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // First sync
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        let first_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();

        // Locally modify the installed file
        fs::write(
            fixture.managed_root().join("agents/coder.md"),
            "# Locally modified",
        )
        .unwrap();

        // Update source too (triggers conflict)
        let agents_dir = fixture.tree_path(src_idx).join("agents");
        fs::write(agents_dir.join("coder.md"), "# Upstream update").unwrap();

        // Re-sync with --force
        let (target2, _) = target::build_with_collisions(&graph, &config).unwrap();
        let sync_diff2 =
            diff::compute(fixture.managed_root(), &first_lock, &target2, false).unwrap();

        let force_options = SyncOptions {
            force: true,
            dry_run: false,
            frozen: false,
        };
        let sync_plan2 = plan::create(&sync_diff2, &force_options, &cache_dir);
        assert!(matches!(
            &sync_plan2.actions[0],
            plan::PlannedAction::Overwrite { .. }
        ));

        let result2 = apply::execute(
            fixture.managed_root(),
            &sync_plan2,
            &force_options,
            &cache_dir,
        )
        .unwrap();
        assert!(matches!(
            result2.outcomes[0].action,
            apply::ActionTaken::Updated
        ));

        // File should have upstream content
        let content = fs::read_to_string(fixture.managed_root().join("agents/coder.md")).unwrap();
        assert_eq!(content, "# Upstream update");
    }

    #[test]
    fn orphan_removed_when_source_drops_item() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(
            &[("coder.md", "# Coder"), ("reviewer.md", "# Reviewer")],
            &[],
        );

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // First sync — install both
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();
        let first_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();

        assert!(fixture.managed_root().join("agents/coder.md").exists());
        assert!(fixture.managed_root().join("agents/reviewer.md").exists());

        // Remove reviewer from source
        fs::remove_file(fixture.tree_path(src_idx).join("agents/reviewer.md")).unwrap();

        // Re-sync
        let (target2, _) = target::build_with_collisions(&graph, &config).unwrap();
        let sync_diff2 =
            diff::compute(fixture.managed_root(), &first_lock, &target2, false).unwrap();

        // Should have one Unchanged and one Orphan
        let orphan_count = sync_diff2
            .items
            .iter()
            .filter(|e| matches!(e, diff::DiffEntry::Orphan { .. }))
            .count();
        assert_eq!(orphan_count, 1);

        let sync_plan2 = plan::create(&sync_diff2, &options, &cache_dir);
        let result2 =
            apply::execute(fixture.managed_root(), &sync_plan2, &options, &cache_dir).unwrap();

        // Reviewer should be removed
        assert!(!fixture.managed_root().join("agents/reviewer.md").exists());
        // Coder should still be there
        assert!(fixture.managed_root().join("agents/coder.md").exists());

        // Check remove outcome
        let removed = result2
            .outcomes
            .iter()
            .any(|o| matches!(o.action, apply::ActionTaken::Removed));
        assert!(removed);
    }

    #[test]
    fn dry_run_produces_plan_without_changes() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[("coder.md", "# Coder")], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();

        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let dry_options = SyncOptions {
            force: false,
            dry_run: true,
            frozen: false,
        };

        let sync_plan = plan::create(&sync_diff, &dry_options, &cache_dir);
        assert!(!sync_plan.actions.is_empty());

        // Execute in dry-run mode
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &dry_options, &cache_dir).unwrap();
        assert!(!result.outcomes.is_empty());

        // No files should have been created
        assert!(!fixture.managed_root().join("agents/coder.md").exists());
    }

    #[test]
    fn lock_written_after_apply() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[("coder.md", "# Coder")], &[]);

        let (graph, config) = make_graph_config(&fixture, vec![("base", src_idx, FilterMode::All)]);

        // Full pipeline minus actual sync() (which needs real config files)
        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();

        let new_lock = crate::lock::build(&graph, &result, &lock, None).unwrap();
        crate::lock::write(fixture.project_root(), &new_lock).unwrap();

        // Verify lock file exists and is valid
        let reloaded = crate::lock::load(fixture.project_root()).unwrap();
        assert_eq!(reloaded.items.len(), 1);
        assert!(reloaded.items.contains_key("agents/coder.md"));

        let item = &reloaded.items["agents/coder.md"];
        assert_eq!(item.kind, ItemKind::Agent);
        assert!(!item.source_checksum.is_empty());
        assert!(!item.installed_checksum.is_empty());
    }

    #[test]
    fn two_sources_no_collision() {
        let mut fixture = TestFixture::new();
        let src_a = fixture.add_source(&[("coder.md", "# Coder from A")], &[]);
        let src_b = fixture.add_source(&[("reviewer.md", "# Reviewer from B")], &[]);

        let (graph, config) = make_graph_config(
            &fixture,
            vec![
                ("source-a", src_a, FilterMode::All),
                ("source-b", src_b, FilterMode::All),
            ],
        );

        let (target, renames) = target::build_with_collisions(&graph, &config).unwrap();
        assert!(renames.is_empty());
        assert_eq!(target.items.len(), 2);

        let lock = LockFile::empty();
        let sync_diff = diff::compute(fixture.managed_root(), &lock, &target, false).unwrap();
        let cache_dir = fixture.project_root().join(".mars/cache/bases");
        let options = SyncOptions {
            force: false,
            dry_run: false,
            frozen: false,
        };
        let sync_plan = plan::create(&sync_diff, &options, &cache_dir);
        let result =
            apply::execute(fixture.managed_root(), &sync_plan, &options, &cache_dir).unwrap();

        assert!(fixture.managed_root().join("agents/coder.md").exists());
        assert!(fixture.managed_root().join("agents/reviewer.md").exists());
        assert_eq!(result.outcomes.len(), 2);
    }

    // === Tests for OnlySkills / OnlyAgents filter in pipeline ===

    #[test]
    fn pipeline_only_skills_filter() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(
            &[("coder.md", "# Coder agent")],
            &[("planning", "# Planning skill")],
        );

        let (graph, config) =
            make_graph_config(&fixture, vec![("base", src_idx, FilterMode::OnlySkills)]);

        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        // Should only have the skill, not the agent
        assert_eq!(target.items.len(), 1);
        assert!(target.items.contains_key("skills/planning"));
    }

    #[test]
    fn pipeline_only_agents_filter() {
        let mut fixture = TestFixture::new();
        // Agent with a skill dependency in frontmatter
        let agent_content = "---\nskills:\n  - planning\n---\n# Coder agent";
        let src_idx = fixture.add_source(
            &[("coder.md", agent_content)],
            &[
                ("planning", "# Planning skill"),
                ("standalone", "# Standalone skill"),
            ],
        );

        let (graph, config) =
            make_graph_config(&fixture, vec![("base", src_idx, FilterMode::OnlyAgents)]);

        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        // Should have the agent + its transitive skill dep, but NOT standalone
        assert_eq!(target.items.len(), 2);
        assert!(target.items.contains_key("agents/coder.md"));
        assert!(target.items.contains_key("skills/planning"));
        assert!(!target.items.contains_key("skills/standalone"));
    }

    #[test]
    fn pipeline_only_agents_no_agents_source() {
        let mut fixture = TestFixture::new();
        let src_idx = fixture.add_source(&[], &[("planning", "# Planning skill")]);

        let (graph, config) =
            make_graph_config(&fixture, vec![("base", src_idx, FilterMode::OnlyAgents)]);

        let (target, _) = target::build_with_collisions(&graph, &config).unwrap();
        // No agents means nothing gets installed
        assert_eq!(target.items.len(), 0);
    }
}