agnix-core 0.20.1

//! Fix application engine for automatic corrections

use crate::diagnostics::{Diagnostic, FIX_CONFIDENCE_MEDIUM_THRESHOLD, Fix, LintResult};
use crate::fs::{FileSystem, RealFileSystem};
use crate::parsers::frontmatter::normalize_line_endings;
use std::collections::{HashMap, HashSet};
use std::path::PathBuf;
use std::sync::Arc;

/// Confidence filter for selecting autofixes.
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum FixApplyMode {
    /// Apply only HIGH-confidence fixes (`>= 0.95`).
    SafeOnly,
    /// Apply HIGH and MEDIUM-confidence fixes (`>= 0.75`).
    SafeAndMedium,
    /// Apply all fixes (including LOW confidence).
    All,
}

/// Options for autofix application.
#[derive(Debug, Clone, Copy, PartialEq)]
pub struct FixApplyOptions {
    pub dry_run: bool,
    pub mode: FixApplyMode,
}

impl FixApplyOptions {
    pub fn new(dry_run: bool, mode: FixApplyMode) -> Self {
        Self { dry_run, mode }
    }
}

/// Result of applying fixes to a file.
///
/// # Line endings
///
/// Both `original` and `fixed` hold LF-normalized content (CRLF and lone CR are
/// converted to LF before fixes are applied). Files on disk that used CRLF endings
/// will be written back with LF endings as a side effect of fix application. This is
/// intentional and consistent with the rest of the validation pipeline.
#[derive(Debug, Clone)]
pub struct FixResult {
    /// Path to the file
    pub path: PathBuf,
    /// Original file content (LF-normalized; may differ from raw on-disk bytes for CRLF files)
    pub original: String,
    /// Content after fixes applied (LF-normalized)
    pub fixed: String,
    /// Descriptions of applied fixes
    pub applied: Vec<String>,
}

impl FixResult {
    /// Check if any fixes were actually applied
    pub fn has_changes(&self) -> bool {
        self.original != self.fixed
    }
}

/// Apply fixes from diagnostics to files
///
/// # Arguments
/// * `diagnostics` - Diagnostics with potential fixes
/// * `dry_run` - If true, compute fixes but don't write files
/// * `safe_only` - If true, only apply fixes marked as safe
///
/// # Returns
/// Vector of fix results, one per file that had fixes
pub fn apply_fixes(
    diagnostics: &[Diagnostic],
    dry_run: bool,
    safe_only: bool,
) -> LintResult<Vec<FixResult>> {
    let mode = if safe_only {
        FixApplyMode::SafeOnly
    } else {
        // Backwards-compatible behavior for this stable API:
        // when `safe_only=false`, apply all fixes.
        FixApplyMode::All
    };
    apply_fixes_with_options(diagnostics, FixApplyOptions::new(dry_run, mode))
}

/// Apply fixes from diagnostics to files with optional FileSystem abstraction
///
/// # Arguments
/// * `diagnostics` - Diagnostics with potential fixes
/// * `dry_run` - If true, compute fixes but don't write files
/// * `safe_only` - If true, only apply fixes marked as safe
/// * `fs` - Optional FileSystem for reading/writing files. If None, uses RealFileSystem.
///
/// # Returns
/// Vector of fix results, one per file that had fixes
pub fn apply_fixes_with_fs(
    diagnostics: &[Diagnostic],
    dry_run: bool,
    safe_only: bool,
    fs: Option<Arc<dyn FileSystem>>,
) -> LintResult<Vec<FixResult>> {
    let mode = if safe_only {
        FixApplyMode::SafeOnly
    } else {
        FixApplyMode::All
    };
    apply_fixes_with_fs_options(diagnostics, FixApplyOptions::new(dry_run, mode), fs)
}

/// Apply fixes using explicit options.
pub fn apply_fixes_with_options(
    diagnostics: &[Diagnostic],
    options: FixApplyOptions,
) -> LintResult<Vec<FixResult>> {
    apply_fixes_with_fs_options(diagnostics, options, None)
}

/// Apply fixes using explicit options and an optional file system abstraction.
///
/// File content is CRLF-normalized before fixes are applied, so byte offsets in
/// [`Fix`] objects must reference LF-normalized positions (as produced by
/// `validate_content` or `validate_file`). Files with CRLF endings
/// will be written back with LF endings.
pub fn apply_fixes_with_fs_options(
    diagnostics: &[Diagnostic],
    options: FixApplyOptions,
    fs: Option<Arc<dyn FileSystem>>,
) -> LintResult<Vec<FixResult>> {
    let fs = fs.unwrap_or_else(|| Arc::new(RealFileSystem));

    // Group diagnostics by file
    let mut by_file: HashMap<PathBuf, Vec<&Diagnostic>> = HashMap::new();
    for diag in diagnostics {
        if diag.has_fixes() {
            by_file.entry(diag.file.clone()).or_default().push(diag);
        }
    }

    let mut results = Vec::new();

    for (path, file_diagnostics) in by_file {
        let raw_content = fs.read_to_string(&path)?;
        // Match on the Cow to avoid a second scan: Borrowed means LF-only (reuse the
        // already-owned String), Owned means normalization was needed.
        let original = match normalize_line_endings(&raw_content) {
            std::borrow::Cow::Borrowed(_) => raw_content,
            std::borrow::Cow::Owned(normalized) => normalized,
        };

        let mut fixes = select_fixes(&file_diagnostics, options.mode);

        if fixes.is_empty() {
            continue;
        }

        // Sort descending to apply from end (preserves earlier positions)
        fixes.sort_by_key(|f| std::cmp::Reverse(f.start_byte));

        let (fixed, applied) = apply_fixes_to_content(&original, &fixes);

        if fixed != original {
            if !options.dry_run {
                fs.write(&path, &fixed)?;
            }

            results.push(FixResult {
                path,
                original,
                fixed,
                applied,
            });
        }
    }

    results.sort_by(|a, b| a.path.cmp(&b.path));

    Ok(results)
}

/// Apply fixes to content string, returning new content and applied descriptions.
/// Fixes must be sorted by start_byte descending to preserve positions.
fn apply_fixes_to_content(content: &str, fixes: &[&Fix]) -> (String, Vec<String>) {
    let mut result = content.to_string();
    let mut applied = Vec::new();
    let mut last_start = usize::MAX;
    let (planned_groups, planned_descriptions) = planned_dependency_keys(content, fixes);

    for fix in fixes {
        if let Some(depends_on) = fix.depends_on.as_deref() {
            let satisfied =
                planned_groups.contains(depends_on) || planned_descriptions.contains(depends_on);
            if !satisfied {
                continue;
            }
        }

        // Check end_byte > start_byte first (more fundamental invariant)
        if fix.end_byte < fix.start_byte {
            // Log: Invalid fix range (end before start)
            continue;
        }
        // Then check bounds
        if fix.start_byte > result.len() || fix.end_byte > result.len() {
            // Log: Fix out of bounds
            continue;
        }
        // Check UTF-8 boundaries
        if !result.is_char_boundary(fix.start_byte) || !result.is_char_boundary(fix.end_byte) {
            // Log: UTF-8 boundary violation - this indicates a bug in fix generation
            // The fix byte offsets don't align with character boundaries
            continue;
        }
        // Skip overlapping fixes (sorted descending, so check against previous fix start)
        if fix.end_byte > last_start {
            // Log: Skipping overlapping fix
            continue;
        }

        result.replace_range(fix.start_byte..fix.end_byte, &fix.replacement);
        applied.push(fix.description.clone());
        last_start = fix.start_byte;
    }

    applied.reverse();

    (result, applied)
}

fn select_fixes<'a>(file_diagnostics: &'a [&'a Diagnostic], mode: FixApplyMode) -> Vec<&'a Fix> {
    let candidates: Vec<&Fix> = file_diagnostics
        .iter()
        .flat_map(|d| d.fixes.iter())
        .filter(|fix| should_apply_by_mode(fix, mode))
        .collect();

    let dependency_resolved = resolve_dependency_candidates(candidates);
    select_group_alternatives(dependency_resolved)
}

fn should_apply_by_mode(fix: &Fix, mode: FixApplyMode) -> bool {
    match mode {
        FixApplyMode::SafeOnly => fix.is_safe(),
        FixApplyMode::SafeAndMedium => fix.confidence_score() >= FIX_CONFIDENCE_MEDIUM_THRESHOLD,
        FixApplyMode::All => true,
    }
}

fn resolve_dependency_candidates(mut fixes: Vec<&Fix>) -> Vec<&Fix> {
    // Cap iterations to the number of fixes with dependencies (+1 for convergence
    // check). This matches the algorithm's actual termination condition better
    // than total fix count, and avoids wasted iterations for large fix sets
    // with shallow dependency chains.
    let deps_count = fixes.iter().filter(|f| f.depends_on.is_some()).count();
    let max_iterations = deps_count.saturating_add(1);
    for _ in 0..max_iterations {
        let groups: HashSet<&str> = fixes.iter().filter_map(|f| f.group.as_deref()).collect();
        let descriptions: HashSet<&str> = fixes.iter().map(|f| f.description.as_str()).collect();
        let before = fixes.len();

        fixes.retain(|fix| match fix.depends_on.as_deref() {
            Some(depends_on) => groups.contains(depends_on) || descriptions.contains(depends_on),
            None => true,
        });

        if fixes.len() == before {
            break;
        }
    }

    fixes
}

fn select_group_alternatives(fixes: Vec<&Fix>) -> Vec<&Fix> {
    let mut selected_groups: HashSet<&str> = HashSet::new();
    let mut selected = Vec::new();

    for fix in fixes {
        if let Some(group) = fix.group.as_deref() {
            if selected_groups.contains(group) {
                continue;
            }
            selected_groups.insert(group);
        }

        selected.push(fix);
    }

    selected
}

fn planned_dependency_keys<'a>(
    content: &str,
    fixes: &[&'a Fix],
) -> (HashSet<&'a str>, HashSet<&'a str>) {
    let mut groups = HashSet::new();
    let mut descriptions = HashSet::new();
    let mut last_start = usize::MAX;

    for fix in fixes {
        if !is_fix_range_applicable(content, fix) {
            continue;
        }

        if fix.end_byte > last_start {
            continue;
        }

        descriptions.insert(fix.description.as_str());
        if let Some(group) = fix.group.as_deref() {
            groups.insert(group);
        }
        last_start = fix.start_byte;
    }

    (groups, descriptions)
}

fn is_fix_range_applicable(content: &str, fix: &Fix) -> bool {
    if fix.end_byte < fix.start_byte {
        return false;
    }

    if fix.start_byte > content.len() || fix.end_byte > content.len() {
        return false;
    }

    content.is_char_boundary(fix.start_byte) && content.is_char_boundary(fix.end_byte)
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::diagnostics::{DiagnosticLevel, Fix};

    fn make_diagnostic(path: &str, fixes: Vec<Fix>) -> Diagnostic {
        Diagnostic {
            level: DiagnosticLevel::Error,
            message: "Test error".to_string(),
            file: PathBuf::from(path),
            line: 1,
            column: 1,
            rule: "TEST-001".to_string(),
            suggestion: None,
            fixes,
            assumption: None,
            metadata: None,
        }
    }

    #[test]
    fn test_fix_single_replacement() {
        let content = "name: Bad_Name";
        let fix = Fix::replace(6, 14, "good-name", "Fix name format", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "name: good-name");
        assert_eq!(applied.len(), 1);
        assert_eq!(applied[0], "Fix name format");
    }

    #[test]
    fn test_fix_insertion() {
        let content = "hello world";
        let fix = Fix::insert(5, " beautiful", "Add word", true);

        let (result, _) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "hello beautiful world");
    }

    #[test]
    fn test_fix_deletion() {
        let content = "hello beautiful world";
        let fix = Fix::delete(5, 15, "Remove word", true);

        let (result, _) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "hello world");
    }

    #[test]
    fn test_fix_multiple_non_overlapping() {
        let content = "aaa bbb ccc";
        let fixes = vec![
            Fix::replace(0, 3, "AAA", "Uppercase first", true),
            Fix::replace(8, 11, "CCC", "Uppercase last", true),
        ];
        let fix_refs: Vec<&Fix> = fixes.iter().collect();

        // Sort descending by start_byte (as apply_fixes does)
        let mut sorted = fix_refs.clone();
        sorted.sort_by_key(|b| std::cmp::Reverse(b.start_byte));

        let (result, applied) = apply_fixes_to_content(content, &sorted);

        assert_eq!(result, "AAA bbb CCC");
        assert_eq!(applied.len(), 2);
    }

    #[test]
    fn test_fix_reverse_order_preserves_positions() {
        // When we have fixes at positions 0-3 and 8-11,
        // applying 8-11 first keeps position 0-3 valid
        let content = "foo bar baz";
        let fixes = vec![
            Fix::replace(0, 3, "FOO", "Fix 1", true),
            Fix::replace(8, 11, "BAZ", "Fix 2", true),
        ];

        // Sort descending (8-11 first, then 0-3)
        let mut sorted: Vec<&Fix> = fixes.iter().collect();
        sorted.sort_by_key(|b| std::cmp::Reverse(b.start_byte));

        let (result, _) = apply_fixes_to_content(content, &sorted);

        assert_eq!(result, "FOO bar BAZ");
    }

    #[test]
    fn test_fix_safe_only_filter() {
        let temp = tempfile::TempDir::new().unwrap();
        let path = temp.path().join("test.md");
        std::fs::write(&path, "name: Bad_Name").unwrap();

        let diagnostics = vec![make_diagnostic(
            path.to_str().unwrap(),
            vec![
                Fix::replace(6, 14, "safe-name", "Safe fix", true),
                Fix::replace(0, 4, "NAME", "Unsafe fix", false),
            ],
        )];

        // With safe_only = true, only the safe fix should apply
        let results = apply_fixes(&diagnostics, false, true).unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "name: safe-name");
        assert_eq!(results[0].applied.len(), 1);
    }

    #[test]
    fn test_fix_mode_safe_and_medium_filters_low() {
        let temp = tempfile::TempDir::new().unwrap();
        let path = temp.path().join("test.md");
        std::fs::write(&path, "abcdef").unwrap();

        let diagnostics = vec![make_diagnostic(
            path.to_str().unwrap(),
            vec![
                Fix::replace_with_confidence(0, 1, "A", "high", 0.99),
                Fix::replace_with_confidence(1, 2, "B", "medium", 0.80),
                Fix::replace_with_confidence(2, 3, "C", "low", 0.20),
            ],
        )];

        let results = apply_fixes_with_options(
            &diagnostics,
            FixApplyOptions::new(false, FixApplyMode::SafeAndMedium),
        )
        .unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "ABcdef");
        assert_eq!(results[0].applied, vec!["high", "medium"]);
    }

    #[test]
    fn test_fix_mode_safe_only_applies_high_only() {
        let temp = tempfile::TempDir::new().unwrap();
        let path = temp.path().join("test.md");
        std::fs::write(&path, "abcdef").unwrap();

        let diagnostics = vec![make_diagnostic(
            path.to_str().unwrap(),
            vec![
                Fix::replace_with_confidence(0, 1, "A", "high", 0.99),
                Fix::replace_with_confidence(1, 2, "B", "medium", 0.80),
                Fix::replace_with_confidence(2, 3, "C", "low", 0.20),
            ],
        )];

        let results = apply_fixes_with_options(
            &diagnostics,
            FixApplyOptions::new(false, FixApplyMode::SafeOnly),
        )
        .unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "Abcdef");
        assert_eq!(results[0].applied, vec!["high"]);
    }

    #[test]
    fn test_fix_group_applies_first_alternative_only() {
        let content = "hello";
        let first = Fix::insert(5, "!", "first", true).with_group("punctuation");
        let second = Fix::insert(5, "?", "second", true).with_group("punctuation");

        // Keep source order to confirm first alternative wins.
        let fixes = vec![&first, &second];
        let (fixed, applied) = apply_fixes_to_content(content, &fixes);

        // Engine-level group handling happens before this function, so emulate selection.
        let diagnostic = make_diagnostic(
            "x.md",
            vec![
                Fix::insert(5, "!", "first", true).with_group("punctuation"),
                Fix::insert(5, "?", "second", true).with_group("punctuation"),
            ],
        );
        let diagnostics = [&diagnostic];
        let selected = select_fixes(&diagnostics, FixApplyMode::All);
        let mut refs = selected;
        refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (selected_fixed, selected_applied) = apply_fixes_to_content(content, &refs);

        assert_eq!(fixed, "hello?!");
        assert_eq!(applied.len(), 2);
        assert_eq!(selected_fixed, "hello!");
        assert_eq!(selected_applied, vec!["first"]);
    }

    #[test]
    fn test_fix_dependency_requires_predecessor() {
        let content = "foo bar";
        let prerequisite = Fix::replace(4, 7, "BAR", "normalize-tail", true).with_group("step1");
        let dependent = Fix::replace(0, 3, "FOO", "normalize-head", true).with_dependency("step1");
        let orphan = Fix::replace(0, 3, "XXX", "orphan", true).with_dependency("missing");

        let mut refs = vec![&prerequisite, &dependent];
        refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (fixed, applied) = apply_fixes_to_content(content, &refs);
        assert_eq!(fixed, "FOO BAR");
        assert_eq!(applied, vec!["normalize-head", "normalize-tail"]);

        let mut orphan_refs = vec![&orphan];
        orphan_refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (orphan_fixed, orphan_applied) = apply_fixes_to_content(content, &orphan_refs);
        assert_eq!(orphan_fixed, content);
        assert!(orphan_applied.is_empty());
    }

    #[test]
    fn test_fix_dependency_not_order_sensitive() {
        let content = "foo bar";
        let prerequisite = Fix::replace(0, 3, "FOO", "normalize-head", true).with_group("step1");
        let dependent = Fix::replace(4, 7, "BAR", "normalize-tail", true).with_dependency("step1");

        // Descending sort puts dependent first, but dependency should still be satisfied.
        let mut refs = vec![&prerequisite, &dependent];
        refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (fixed, applied) = apply_fixes_to_content(content, &refs);

        assert_eq!(fixed, "FOO BAR");
        assert_eq!(applied, vec!["normalize-head", "normalize-tail"]);
    }

    #[test]
    fn test_fix_dependency_can_reference_description() {
        let content = "foo bar";
        let prerequisite = Fix::replace(0, 3, "FOO", "normalize-head", true);
        let dependent =
            Fix::replace(4, 7, "BAR", "normalize-tail", true).with_dependency("normalize-head");

        let mut refs = vec![&prerequisite, &dependent];
        refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (fixed, applied) = apply_fixes_to_content(content, &refs);

        assert_eq!(fixed, "FOO BAR");
        assert_eq!(applied, vec!["normalize-head", "normalize-tail"]);
    }

    #[test]
    fn test_fix_dependency_skips_when_prerequisite_would_be_invalid() {
        let content = "foo bar";
        let prerequisite =
            Fix::replace(10, 11, "X", "invalid-prerequisite", true).with_group("step1");
        let dependent = Fix::replace(4, 7, "BAR", "normalize-tail", true).with_dependency("step1");

        let mut refs = vec![&prerequisite, &dependent];
        refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));
        let (fixed, applied) = apply_fixes_to_content(content, &refs);

        assert_eq!(fixed, content);
        assert!(applied.is_empty());
    }

    #[test]
    fn test_fix_group_falls_back_when_first_candidate_is_removed() {
        let diagnostic = make_diagnostic(
            "x.md",
            vec![
                Fix::insert(5, "!", "first", true)
                    .with_group("punctuation")
                    .with_dependency("missing"),
                Fix::insert(5, "?", "second", true).with_group("punctuation"),
            ],
        );
        let diagnostics = [&diagnostic];
        let selected = select_fixes(&diagnostics, FixApplyMode::All);

        assert_eq!(selected.len(), 1);
        assert_eq!(selected[0].description, "second");
    }

    #[test]
    fn test_fix_dry_run_no_write() {
        let temp = tempfile::TempDir::new().unwrap();
        let path = temp.path().join("test.md");
        let original = "name: Bad_Name";
        std::fs::write(&path, original).unwrap();

        let diagnostics = vec![make_diagnostic(
            path.to_str().unwrap(),
            vec![Fix::replace(6, 14, "good-name", "Fix name", true)],
        )];

        // Dry run
        let results = apply_fixes(&diagnostics, true, false).unwrap();

        // Results should show the fix
        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "name: good-name");

        // But file should be unchanged
        let file_content = std::fs::read_to_string(&path).unwrap();
        assert_eq!(file_content, original);
    }

    #[test]
    fn test_fix_actual_write() {
        let temp = tempfile::TempDir::new().unwrap();
        let path = temp.path().join("test.md");
        std::fs::write(&path, "name: Bad_Name").unwrap();

        let diagnostics = vec![make_diagnostic(
            path.to_str().unwrap(),
            vec![Fix::replace(6, 14, "good-name", "Fix name", true)],
        )];

        // Actually apply
        let results = apply_fixes(&diagnostics, false, false).unwrap();

        assert_eq!(results.len(), 1);

        // File should be modified
        let file_content = std::fs::read_to_string(&path).unwrap();
        assert_eq!(file_content, "name: good-name");
    }

    #[test]
    fn test_fix_invalid_positions_skipped() {
        let content = "short";
        let fix = Fix::replace(100, 200, "won't apply", "Bad fix", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "short");
        assert!(applied.is_empty());
    }

    #[test]
    fn test_fix_empty_diagnostics() {
        let results = apply_fixes(&[], false, false).unwrap();
        assert!(results.is_empty());
    }

    #[test]
    fn test_fix_no_fixes_in_diagnostics() {
        let diagnostics = vec![Diagnostic {
            level: DiagnosticLevel::Error,
            message: "No fix available".to_string(),
            file: PathBuf::from("test.md"),
            line: 1,
            column: 1,
            rule: "TEST-001".to_string(),
            suggestion: None,
            fixes: Vec::new(),
            assumption: None,
            metadata: None,
        }];

        let results = apply_fixes(&diagnostics, false, false).unwrap();
        assert!(results.is_empty());
    }

    #[test]
    fn test_fix_result_has_changes() {
        let result_with_changes = FixResult {
            path: PathBuf::from("test.md"),
            original: "old".to_string(),
            fixed: "new".to_string(),
            applied: vec!["Fix".to_string()],
        };
        assert!(result_with_changes.has_changes());

        let result_no_changes = FixResult {
            path: PathBuf::from("test.md"),
            original: "same".to_string(),
            fixed: "same".to_string(),
            applied: vec![],
        };
        assert!(!result_no_changes.has_changes());
    }

    #[test]
    fn test_fix_overlapping_skipped() {
        let content = "hello world";
        // Overlapping fixes: first at 6-11, second at 4-8
        // Sorted descending: 6-11 first, then 4-8
        // 4-8 overlaps with 6-11 (end_byte 8 > start 6), should be skipped
        let fixes = vec![
            Fix::replace(6, 11, "universe", "Fix 1", true),
            Fix::replace(4, 8, "XXX", "Fix 2 overlaps", true),
        ];

        let mut sorted: Vec<&Fix> = fixes.iter().collect();
        sorted.sort_by_key(|b| std::cmp::Reverse(b.start_byte));

        let (result, applied) = apply_fixes_to_content(content, &sorted);

        assert_eq!(result, "hello universe");
        assert_eq!(applied.len(), 1);
        assert_eq!(applied[0], "Fix 1");
    }

    // ===== MockFileSystem Integration Tests =====

    #[test]
    fn test_apply_fixes_with_mock_fs_dry_run() {
        use crate::fs::MockFileSystem;

        let mock_fs = MockFileSystem::new();
        mock_fs.add_file("/project/test.md", "name: Bad_Name");

        let diagnostics = vec![make_diagnostic(
            "/project/test.md",
            vec![Fix::replace(6, 14, "good-name", "Fix name", true)],
        )];

        // Dry run with mock filesystem
        let results =
            apply_fixes_with_fs(&diagnostics, true, false, Some(Arc::new(mock_fs))).unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].original, "name: Bad_Name");
        assert_eq!(results[0].fixed, "name: good-name");
        assert!(results[0].has_changes());

        // File should be unchanged (dry run)
        // Note: We can't verify this directly since we passed ownership,
        // but the logic is tested - dry_run=true means no write() call
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_actual_write() {
        use crate::fs::{FileSystem, MockFileSystem};

        let mock_fs = Arc::new(MockFileSystem::new());
        mock_fs.add_file("/project/test.md", "name: Bad_Name");

        let diagnostics = vec![make_diagnostic(
            "/project/test.md",
            vec![Fix::replace(6, 14, "good-name", "Fix name", true)],
        )];

        // Clone as trait object for apply_fixes_with_fs
        let fs_clone: Arc<dyn FileSystem> = Arc::clone(&mock_fs) as Arc<dyn FileSystem>;

        // Actually apply with mock filesystem
        let results = apply_fixes_with_fs(&diagnostics, false, false, Some(fs_clone)).unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "name: good-name");

        // Verify mock filesystem was updated
        let content = mock_fs
            .read_to_string(std::path::Path::new("/project/test.md"))
            .unwrap();
        assert_eq!(content, "name: good-name");
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_safe_only() {
        use crate::fs::{FileSystem, MockFileSystem};

        let mock_fs = Arc::new(MockFileSystem::new());
        mock_fs.add_file("/project/test.md", "name: Bad_Name");

        let diagnostics = vec![make_diagnostic(
            "/project/test.md",
            vec![
                Fix::replace(6, 14, "safe-name", "Safe fix", true),
                Fix::replace(0, 4, "NAME", "Unsafe fix", false),
            ],
        )];

        // Clone as trait object for apply_fixes_with_fs
        let fs_clone: Arc<dyn FileSystem> = Arc::clone(&mock_fs) as Arc<dyn FileSystem>;

        // Apply with safe_only = true
        let results = apply_fixes_with_fs(&diagnostics, false, true, Some(fs_clone)).unwrap();

        assert_eq!(results.len(), 1);
        // Only safe fix should be applied
        assert_eq!(results[0].fixed, "name: safe-name");
        assert_eq!(results[0].applied.len(), 1);
        assert_eq!(results[0].applied[0], "Safe fix");

        // Verify mock filesystem reflects only safe fix
        let content = mock_fs
            .read_to_string(std::path::Path::new("/project/test.md"))
            .unwrap();
        assert_eq!(content, "name: safe-name");
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_multiple_files() {
        use crate::fs::{FileSystem, MockFileSystem};

        let mock_fs = Arc::new(MockFileSystem::new());
        mock_fs.add_file("/project/file1.md", "old1");
        mock_fs.add_file("/project/file2.md", "old2");

        let diagnostics = vec![
            make_diagnostic(
                "/project/file1.md",
                vec![Fix::replace(0, 4, "new1", "Fix file1", true)],
            ),
            make_diagnostic(
                "/project/file2.md",
                vec![Fix::replace(0, 4, "new2", "Fix file2", true)],
            ),
        ];

        // Clone as trait object for apply_fixes_with_fs
        let fs_clone: Arc<dyn FileSystem> = Arc::clone(&mock_fs) as Arc<dyn FileSystem>;

        let results = apply_fixes_with_fs(&diagnostics, false, false, Some(fs_clone)).unwrap();

        assert_eq!(results.len(), 2);

        // Verify both files were updated
        let content1 = mock_fs
            .read_to_string(std::path::Path::new("/project/file1.md"))
            .unwrap();
        let content2 = mock_fs
            .read_to_string(std::path::Path::new("/project/file2.md"))
            .unwrap();

        assert_eq!(content1, "new1");
        assert_eq!(content2, "new2");
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_file_not_found() {
        use crate::fs::MockFileSystem;

        let mock_fs = MockFileSystem::new();
        // Don't add the file - it should error

        let diagnostics = vec![make_diagnostic(
            "/project/nonexistent.md",
            vec![Fix::replace(0, 4, "new", "Fix", true)],
        )];

        let result = apply_fixes_with_fs(&diagnostics, false, false, Some(Arc::new(mock_fs)));

        assert!(result.is_err());
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_no_changes() {
        use crate::fs::MockFileSystem;

        let mock_fs = MockFileSystem::new();
        mock_fs.add_file("/project/test.md", "unchanged");

        // Diagnostic with no fixes
        let diagnostics = vec![Diagnostic {
            level: DiagnosticLevel::Error,
            message: "No fix available".to_string(),
            file: PathBuf::from("/project/test.md"),
            line: 1,
            column: 1,
            rule: "TEST-001".to_string(),
            suggestion: None,
            fixes: Vec::new(),
            assumption: None,
            metadata: None,
        }];

        let results =
            apply_fixes_with_fs(&diagnostics, false, false, Some(Arc::new(mock_fs))).unwrap();

        // No fixes means no results
        assert!(results.is_empty());
    }

    // ===== Edge Case: Ordering and Overlap Tests =====

    #[test]
    fn test_fix_three_non_overlapping_descending() {
        let content = "aaaa_bbbb_cccc_dddd_eeee_ffff";
        // Fixes at positions 20-24, 10-14, 0-4 (already sorted descending)
        let fixes = vec![
            Fix::replace(20, 24, "EEEE", "Fix third", true),
            Fix::replace(10, 14, "CCCC", "Fix second", true),
            Fix::replace(0, 4, "AAAA", "Fix first", true),
        ];
        let fix_refs: Vec<&Fix> = fixes.iter().collect();

        let (result, applied) = apply_fixes_to_content(content, &fix_refs);

        assert_eq!(applied.len(), 3);
        assert!(result.contains("AAAA"));
        assert!(result.contains("CCCC"));
        assert!(result.contains("EEEE"));
    }

    #[test]
    fn test_fix_overlapping_middle_skipped() {
        let content = "0123456789abcdef";
        // Sorted descending: 10-14 first, then 6-12 (overlaps), then 0-4
        let fixes = vec![
            Fix::replace(10, 14, "XX", "Fix at 10", true),
            Fix::replace(6, 12, "YY", "Fix at 6 (overlaps)", true),
            Fix::replace(0, 4, "ZZ", "Fix at 0", true),
        ];
        let fix_refs: Vec<&Fix> = fixes.iter().collect();

        let (result, applied) = apply_fixes_to_content(content, &fix_refs);

        // Fix at 10-14 applied, fix at 6-12 skipped (end_byte 12 > last_start 10),
        // fix at 0-4 applied (end_byte 4 < last_start 10, but after the overlap skip,
        // last_start is still 10 from the first fix)
        assert_eq!(
            applied.len(),
            2,
            "Only two non-overlapping fixes should apply"
        );
        assert!(result.contains("XX"), "Fix at 10-14 should be applied");
        assert!(result.contains("ZZ"), "Fix at 0-4 should be applied");
        assert!(
            !result.contains("YY"),
            "Overlapping fix at 6-12 should be skipped"
        );
    }

    #[test]
    fn test_fix_adjacent_fixes() {
        let content = "hello world";
        // Sorted descending: (5,6) first, then (0,5)
        // end_byte 5 == last_start 5 -> NOT > so both should apply
        let fixes = vec![
            Fix::replace(5, 6, "_", "Replace space", true),
            Fix::replace(0, 5, "HELLO", "Uppercase first word", true),
        ];
        let fix_refs: Vec<&Fix> = fixes.iter().collect();

        let (result, applied) = apply_fixes_to_content(content, &fix_refs);

        assert_eq!(applied.len(), 2, "Adjacent fixes should both apply");
        assert_eq!(result, "HELLO_world");
    }

    #[test]
    fn test_fix_same_position_insertions() {
        let content = "hello";
        // Two insertions at the same position. Their application order depends on their
        // order in the slice, as the sort by `start_byte` is stable.
        let fixes = vec![
            Fix::insert(5, "!", "Add exclamation", true),
            Fix::insert(5, "?", "Add question", true),
        ];
        let mut fix_refs: Vec<&Fix> = fixes.iter().collect();
        // `apply_fixes_to_content` expects fixes to be sorted descending by start_byte.
        fix_refs.sort_by_key(|b| std::cmp::Reverse(b.start_byte));

        let (result, applied) = apply_fixes_to_content(content, &fix_refs);

        assert_eq!(
            applied.len(),
            2,
            "Same-position insertions should both apply"
        );

        // The fixes are applied in the order they appear in the sorted slice.
        // Since the sort is stable for equal `start_byte`, "!" is applied first, then "?".
        // 1. "hello" -> "hello!"
        // 2. "hello!" -> "hello?!" (at index 5 of the modified string)
        assert_eq!(result, "hello?!");
    }

    #[test]
    fn test_fix_length_changing_preserves_positions() {
        let content = "short___long_text";
        // Sorted descending: 12-17 first, then 0-5
        let fixes = vec![
            Fix::replace(12, 17, "replacement_that_is_longer", "Fix second", true),
            Fix::replace(0, 5, "S", "Fix first", true),
        ];
        let fix_refs: Vec<&Fix> = fixes.iter().collect();

        let (result, applied) = apply_fixes_to_content(content, &fix_refs);

        assert_eq!(applied.len(), 2, "Both fixes should apply");
        assert!(
            result.starts_with("S"),
            "First 5 chars should be replaced with 'S'"
        );
        assert!(
            result.contains("replacement_that_is_longer"),
            "Later range should be replaced"
        );
    }

    #[test]
    fn test_fix_end_before_start_skipped() {
        let content = "hello";
        // Invalid fix: start_byte > end_byte (end_byte < start_byte)
        let fix = Fix {
            start_byte: 3,
            end_byte: 1,
            replacement: "X".to_string(),
            description: "Invalid fix".to_string(),
            safe: true,
            confidence: Some(1.0),
            group: None,
            depends_on: None,
        };

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "hello", "Content should be unchanged");
        assert!(applied.is_empty(), "Invalid fix should be skipped");
    }

    #[test]
    fn test_fix_unicode_content_boundaries() {
        // \u{00e9} is precomposed e-acute: 2 bytes (0xc3, 0xa9)
        let content = "caf\u{00e9} is great";
        // 'c'=0, 'a'=1, 'f'=2, '\u{00e9}'=3-4 (2 bytes), ' '=5
        // Fix byte 3 to 5 (the e-acute), replace with "e"
        let fix = Fix::replace(3, 5, "e", "Normalize accent", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "cafe is great");
        assert_eq!(applied.len(), 1);
    }

    #[test]
    fn test_fix_crlf_content() {
        let content = "hello\r\nworld";
        // Replace \r\n (bytes 5-7) with \n
        let fix = Fix::replace(5, 7, "\n", "Normalize line ending", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "hello\nworld");
        assert_eq!(applied.len(), 1);
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_crlf_normalization() {
        // Verify that apply_fixes_with_fs_options normalizes CRLF before applying fixes.
        // The fix byte offsets are computed against LF-normalized content (as validators see it).
        use crate::fs::MockFileSystem;

        let mock_fs = MockFileSystem::new();
        // File on disk has CRLF endings: "name:\r\n bad-name"
        // After normalization: "name:\n bad-name"
        //   byte 0..5 = "name:", byte 5 = '\n', byte 6 = ' ', byte 7..15 = "bad-name"
        // Fix replaces "bad-name" (bytes 7..15 in normalized form) with "good-name"
        mock_fs.add_file("/project/skill.md", "name:\r\n bad-name");

        let diagnostics = vec![make_diagnostic(
            "/project/skill.md",
            vec![Fix::replace(7, 15, "good-name", "Fix name", true)],
        )];

        let results =
            apply_fixes_with_fs(&diagnostics, true, false, Some(Arc::new(mock_fs))).unwrap();

        assert_eq!(results.len(), 1, "Should produce one FixResult");
        assert!(
            !results[0].original.contains('\r'),
            "FixResult.original should be LF-normalized (no \\r)"
        );
        assert_eq!(results[0].original, "name:\n bad-name");
        assert_eq!(results[0].fixed, "name:\n good-name");
        assert!(results[0].has_changes());
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_crlf_no_actual_changes() {
        // A CRLF file where the only applicable fix leaves content unchanged after normalization
        // should not appear in FixResult. This exercises the normalization code path
        // (the file IS read and normalize_line_endings IS called) via a fix that produces
        // no net change on the normalized content.
        use crate::fs::{FileSystem, MockFileSystem};

        let mock_fs = Arc::new(MockFileSystem::new());
        // CRLF file: after normalization "name:\n good-name" - fix replaces "good-name" with itself
        mock_fs.add_file("/project/skill.md", "name:\r\n good-name");

        let fs_clone: Arc<dyn FileSystem> = Arc::clone(&mock_fs) as Arc<dyn FileSystem>;

        let diagnostics = vec![make_diagnostic(
            "/project/skill.md",
            // Replace "good-name" (bytes 7..16 in normalized "name:\n good-name") with the same text
            vec![Fix::replace(7, 16, "good-name", "No-op fix", true)],
        )];

        let results = apply_fixes_with_fs(&diagnostics, false, false, Some(fs_clone)).unwrap();

        // fixed == original because the fix produces no net change: no FixResult emitted
        assert!(
            results.is_empty(),
            "No FixResult should be emitted when fix produces no net change on normalized content"
        );
    }

    #[test]
    fn test_apply_fixes_with_mock_fs_crlf_actual_write() {
        // Verify the non-dry-run path: apply_fixes_with_fs writes LF-normalized content to disk.
        use crate::fs::{FileSystem, MockFileSystem};

        let mock_fs = Arc::new(MockFileSystem::new());
        // File on disk has CRLF endings
        mock_fs.add_file("/project/skill.md", "name:\r\n bad-name");

        let fs_clone: Arc<dyn FileSystem> = Arc::clone(&mock_fs) as Arc<dyn FileSystem>;

        let diagnostics = vec![make_diagnostic(
            "/project/skill.md",
            vec![Fix::replace(7, 15, "good-name", "Fix name", true)],
        )];

        let results = apply_fixes_with_fs(&diagnostics, false, false, Some(fs_clone)).unwrap();

        assert_eq!(results.len(), 1);
        assert_eq!(results[0].fixed, "name:\n good-name");

        // The written file should contain LF-normalized content
        let written = mock_fs
            .read_to_string(std::path::Path::new("/project/skill.md"))
            .unwrap();
        assert!(
            !written.contains('\r'),
            "Written file should have no \\r (LF-normalized)"
        );
        assert_eq!(written, "name:\n good-name");
    }

    #[test]
    fn test_fix_utf8_boundary_skip() {
        // \u{00e9} = 2 bytes: 0xc3 at byte 3, 0xa9 at byte 4
        let content = "caf\u{00e9}";
        // Fix starting at byte 4 (mid-codepoint continuation byte) should be skipped
        let fix = Fix::replace(4, 5, "X", "Mid-codepoint fix", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(
            result, "caf\u{00e9}",
            "Content should be unchanged when fix targets mid-codepoint"
        );
        assert!(
            applied.is_empty(),
            "Fix at non-char-boundary should be skipped"
        );
    }

    #[test]
    fn test_fix_replacement_with_unicode() {
        let content = "hello world";
        let fix = Fix::replace(6, 11, "\u{4e16}\u{754c}", "Replace with CJK", true);

        let (result, applied) = apply_fixes_to_content(content, &[&fix]);

        assert_eq!(result, "hello \u{4e16}\u{754c}");
        assert_eq!(applied.len(), 1);
    }
}