@machina.ai/cell-cli-core 1.0.13-rc9 → 1.0.21-rc1

package/dist/src/utils/memoryImportProcessor.test.js

@@ -6,14 +6,76 @@
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
 import * as fs from 'fs/promises';
 import * as path from 'path';
+import { marked } from 'marked';
 import { processImports, validateImportPath } from './memoryImportProcessor.js';
-// Mock fs/promises
+// Helper function to create platform-agnostic test paths
+function testPath(...segments) {
+    // Start with the first segment as is (might be an absolute path on Windows)
+    let result = segments[0];
+    // Join remaining segments with the platform-specific separator
+    for (let i = 1; i < segments.length; i++) {
+        if (segments[i].startsWith('/') || segments[i].startsWith('\\')) {
+            // If segment starts with a separator, remove the trailing separator from the result
+            result = path.normalize(result.replace(/[\\/]+$/, '') + segments[i]);
+        }
+        else {
+            // Otherwise join with the platform separator
+            result = path.join(result, segments[i]);
+        }
+    }
+    return path.normalize(result);
+}
 vi.mock('fs/promises');
 const mockedFs = vi.mocked(fs);
 // Mock console methods to capture warnings
 const originalConsoleWarn = console.warn;
 const originalConsoleError = console.error;
 const originalConsoleDebug = console.debug;
+// Helper functions using marked for parsing and validation
+const parseMarkdown = (content) => marked.lexer(content);
+const findMarkdownComments = (content) => {
+    const tokens = parseMarkdown(content);
+    const comments = [];
+    function walkTokens(tokenList) {
+        for (const token of tokenList) {
+            const t = token;
+            if (t.type === 'html' && t.raw.includes('<!--')) {
+                comments.push(t.raw.trim());
+            }
+            if (t.tokens) {
+                walkTokens(t.tokens);
+            }
+        }
+    }
+    walkTokens(tokens);
+    return comments;
+};
+const findCodeBlocks = (content) => {
+    const tokens = parseMarkdown(content);
+    const codeBlocks = [];
+    function walkTokens(tokenList) {
+        for (const token of tokenList) {
+            const t = token;
+            if (t.type === 'code') {
+                codeBlocks.push({
+                    type: 'code_block',
+                    content: t.text,
+                });
+            }
+            else if (t.type === 'codespan') {
+                codeBlocks.push({
+                    type: 'inline_code',
+                    content: t.text,
+                });
+            }
+            if (t.tokens) {
+                walkTokens(t.tokens);
+            }
+        }
+    }
+    walkTokens(tokens);
+    return codeBlocks;
+};
 describe('memoryImportProcessor', () => {
     beforeEach(() => {
         vi.clearAllMocks();
@@ -31,27 +93,47 @@ describe('memoryImportProcessor', () => {
     describe('processImports', () => {
         it('should process basic md file imports', async () => {
             const content = 'Some content @./test.md more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const importedContent = '# Imported Content\nThis is imported.';
             mockedFs.access.mockResolvedValue(undefined);
             mockedFs.readFile.mockResolvedValue(importedContent);
             const result = await processImports(content, basePath, true);
-            expect(result).toContain('<!-- Imported from: ./test.md -->');
-            expect(result).toContain(importedContent);
-            expect(result).toContain('<!-- End of import from: ./test.md -->');
+            // Use marked to find HTML comments (import markers)
+            const comments = findMarkdownComments(result.content);
+            expect(comments.some((c) => c.includes('Imported from: ./test.md'))).toBe(true);
+            expect(comments.some((c) => c.includes('End of import from: ./test.md'))).toBe(true);
+            // Verify the imported content is present
+            expect(result.content).toContain(importedContent);
+            // Verify the markdown structure is valid
+            const tokens = parseMarkdown(result.content);
+            expect(tokens).toBeDefined();
+            expect(tokens.length).toBeGreaterThan(0);
             expect(mockedFs.readFile).toHaveBeenCalledWith(path.resolve(basePath, './test.md'), 'utf-8');
         });
-        it('should warn and fail for non-md file imports', async () => {
+        it('should import non-md files just like md files', async () => {
             const content = 'Some content @./instructions.txt more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
+            const importedContent = '# Instructions\nThis is a text file with markdown.';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile.mockResolvedValue(importedContent);
             const result = await processImports(content, basePath, true);
-            expect(console.warn).toHaveBeenCalledWith('[WARN] [ImportProcessor]', 'Import processor only supports .md files. Attempting to import non-md file: ./instructions.txt. This will fail.');
-            expect(result).toContain('<!-- Import failed: ./instructions.txt - Only .md files are supported -->');
-            expect(mockedFs.readFile).not.toHaveBeenCalled();
+            // Use marked to find import comments
+            const comments = findMarkdownComments(result.content);
+            expect(comments.some((c) => c.includes('Imported from: ./instructions.txt'))).toBe(true);
+            expect(comments.some((c) => c.includes('End of import from: ./instructions.txt'))).toBe(true);
+            // Use marked to parse and validate the imported content structure
+            const tokens = parseMarkdown(result.content);
+            // Find headers in the parsed content
+            const headers = tokens.filter((token) => token.type === 'heading');
+            expect(headers.some((h) => h.text === 'Instructions')).toBe(true);
+            // Verify the imported content is present
+            expect(result.content).toContain(importedContent);
+            expect(console.warn).not.toHaveBeenCalled();
+            expect(mockedFs.readFile).toHaveBeenCalledWith(path.resolve(basePath, './instructions.txt'), 'utf-8');
         });
         it('should handle circular imports', async () => {
             const content = 'Content @./circular.md more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const circularContent = 'Circular @./main.md content';
             mockedFs.access.mockResolvedValue(undefined);
             mockedFs.readFile.mockResolvedValue(circularContent);
@@ -60,23 +142,23 @@ describe('memoryImportProcessor', () => {
                 processedFiles: new Set(),
                 maxDepth: 10,
                 currentDepth: 0,
-                currentFile: '/test/path/main.md', // Simulate we're processing main.md
+                currentFile: testPath('test', 'path', 'main.md'), // Simulate we're processing main.md
             };
             const result = await processImports(content, basePath, true, importState);
             // The circular import should be detected when processing the nested import
-            expect(result).toContain('<!-- Circular import detected: ./main.md -->');
+            expect(result.content).toContain('<!-- File already processed: ./main.md -->');
         });
         it('should handle file not found errors', async () => {
             const content = 'Content @./nonexistent.md more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             mockedFs.access.mockRejectedValue(new Error('File not found'));
             const result = await processImports(content, basePath, true);
-            expect(result).toContain('<!-- Import failed: ./nonexistent.md - File not found -->');
+            expect(result.content).toContain('<!-- Import failed: ./nonexistent.md - File not found -->');
             expect(console.error).toHaveBeenCalledWith('[ERROR] [ImportProcessor]', 'Failed to import ./nonexistent.md: File not found');
         });
         it('should respect max depth limit', async () => {
             const content = 'Content @./deep.md more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const deepContent = 'Deep @./deeper.md content';
             mockedFs.access.mockResolvedValue(undefined);
             mockedFs.readFile.mockResolvedValue(deepContent);
@@ -87,11 +169,11 @@ describe('memoryImportProcessor', () => {
             };
             const result = await processImports(content, basePath, true, importState);
             expect(console.warn).toHaveBeenCalledWith('[WARN] [ImportProcessor]', 'Maximum import depth (1) reached. Stopping import processing.');
-            expect(result).toBe(content);
+            expect(result.content).toBe(content);
         });
         it('should handle nested imports recursively', async () => {
             const content = 'Main @./nested.md content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const nestedContent = 'Nested @./inner.md content';
             const innerContent = 'Inner content';
             mockedFs.access.mockResolvedValue(undefined);
@@ -99,22 +181,22 @@ describe('memoryImportProcessor', () => {
                 .mockResolvedValueOnce(nestedContent)
                 .mockResolvedValueOnce(innerContent);
             const result = await processImports(content, basePath, true);
-            expect(result).toContain('<!-- Imported from: ./nested.md -->');
-            expect(result).toContain('<!-- Imported from: ./inner.md -->');
-            expect(result).toContain(innerContent);
+            expect(result.content).toContain('<!-- Imported from: ./nested.md -->');
+            expect(result.content).toContain('<!-- Imported from: ./inner.md -->');
+            expect(result.content).toContain(innerContent);
         });
         it('should handle absolute paths in imports', async () => {
             const content = 'Content @/absolute/path/file.md more content';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const importedContent = 'Absolute path content';
             mockedFs.access.mockResolvedValue(undefined);
             mockedFs.readFile.mockResolvedValue(importedContent);
             const result = await processImports(content, basePath, true);
-            expect(result).toContain('<!-- Import failed: /absolute/path/file.md - Path traversal attempt -->');
+            expect(result.content).toContain('<!-- Import failed: /absolute/path/file.md - Path traversal attempt -->');
         });
         it('should handle multiple imports in same content', async () => {
             const content = 'Start @./first.md middle @./second.md end';
-            const basePath = '/test/path';
+            const basePath = testPath('test', 'path');
             const firstContent = 'First content';
             const secondContent = 'Second content';
             mockedFs.access.mockResolvedValue(undefined);
@@ -122,48 +204,508 @@ describe('memoryImportProcessor', () => {
                 .mockResolvedValueOnce(firstContent)
                 .mockResolvedValueOnce(secondContent);
             const result = await processImports(content, basePath, true);
-            expect(result).toContain('<!-- Imported from: ./first.md -->');
-            expect(result).toContain('<!-- Imported from: ./second.md -->');
-            expect(result).toContain(firstContent);
-            expect(result).toContain(secondContent);
+            expect(result.content).toContain('<!-- Imported from: ./first.md -->');
+            expect(result.content).toContain('<!-- Imported from: ./second.md -->');
+            expect(result.content).toContain(firstContent);
+            expect(result.content).toContain(secondContent);
+        });
+        it('should ignore imports inside code blocks', async () => {
+            const content = [
+                'Normal content @./should-import.md',
+                '```',
+                'code block with @./should-not-import.md',
+                '```',
+                'More content @./should-import2.md',
+            ].join('\n');
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const importedContent1 = 'Imported 1';
+            const importedContent2 = 'Imported 2';
+            // Only the imports outside code blocks should be processed
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(importedContent1)
+                .mockResolvedValueOnce(importedContent2);
+            const result = await processImports(content, basePath, true, undefined, projectRoot);
+            // Use marked to verify imported content is present
+            expect(result.content).toContain(importedContent1);
+            expect(result.content).toContain(importedContent2);
+            // Use marked to find code blocks and verify the import wasn't processed
+            const codeBlocks = findCodeBlocks(result.content);
+            const hasUnprocessedImport = codeBlocks.some((block) => block.content.includes('@./should-not-import.md'));
+            expect(hasUnprocessedImport).toBe(true);
+            // Verify no import comment was created for the code block import
+            const comments = findMarkdownComments(result.content);
+            expect(comments.some((c) => c.includes('should-not-import.md'))).toBe(false);
+        });
+        it('should ignore imports inside inline code', async () => {
+            const content = [
+                'Normal content @./should-import.md',
+                '`code with import @./should-not-import.md`',
+                'More content @./should-import2.md',
+            ].join('\n');
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const importedContent1 = 'Imported 1';
+            const importedContent2 = 'Imported 2';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(importedContent1)
+                .mockResolvedValueOnce(importedContent2);
+            const result = await processImports(content, basePath, true, undefined, projectRoot);
+            // Verify imported content is present
+            expect(result.content).toContain(importedContent1);
+            expect(result.content).toContain(importedContent2);
+            // Use marked to find inline code spans
+            const codeBlocks = findCodeBlocks(result.content);
+            const inlineCodeSpans = codeBlocks.filter((block) => block.type === 'inline_code');
+            // Verify the inline code span still contains the unprocessed import
+            expect(inlineCodeSpans.some((span) => span.content.includes('@./should-not-import.md'))).toBe(true);
+            // Verify no import comments were created for inline code imports
+            const comments = findMarkdownComments(result.content);
+            expect(comments.some((c) => c.includes('should-not-import.md'))).toBe(false);
+        });
+        it('should handle nested tokens and non-unique content correctly', async () => {
+            // This test verifies the robust findCodeRegions implementation
+            // that recursively walks the token tree and handles non-unique content
+            const content = [
+                'Normal content @./should-import.md',
+                'Paragraph with `inline code @./should-not-import.md` and more text.',
+                'Another paragraph with the same `inline code @./should-not-import.md` text.',
+                'More content @./should-import2.md',
+            ].join('\n');
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const importedContent1 = 'Imported 1';
+            const importedContent2 = 'Imported 2';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(importedContent1)
+                .mockResolvedValueOnce(importedContent2);
+            const result = await processImports(content, basePath, true, undefined, projectRoot);
+            // Should process imports outside code regions
+            expect(result.content).toContain(importedContent1);
+            expect(result.content).toContain(importedContent2);
+            // Should preserve imports inside inline code (both occurrences)
+            expect(result.content).toContain('`inline code @./should-not-import.md`');
+            // Should not have processed the imports inside code regions
+            expect(result.content).not.toContain('<!-- Imported from: ./should-not-import.md -->');
+        });
+        it('should allow imports from parent and subdirectories within project root', async () => {
+            const content = 'Parent import: @../parent.md Subdir import: @./components/sub.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const importedParent = 'Parent file content';
+            const importedSub = 'Subdir file content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(importedParent)
+                .mockResolvedValueOnce(importedSub);
+            const result = await processImports(content, basePath, true, undefined, projectRoot);
+            expect(result.content).toContain(importedParent);
+            expect(result.content).toContain(importedSub);
+        });
+        it('should reject imports outside project root', async () => {
+            const content = 'Outside import: @../../../etc/passwd';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const result = await processImports(content, basePath, true, undefined, projectRoot);
+            expect(result.content).toContain('<!-- Import failed: ../../../etc/passwd - Path traversal attempt -->');
+        });
+        it('should build import tree structure', async () => {
+            const content = 'Main content @./nested.md @./simple.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const nestedContent = 'Nested @./inner.md content';
+            const simpleContent = 'Simple content';
+            const innerContent = 'Inner content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(nestedContent)
+                .mockResolvedValueOnce(simpleContent)
+                .mockResolvedValueOnce(innerContent);
+            const result = await processImports(content, basePath, true);
+            // Use marked to find and validate import comments
+            const comments = findMarkdownComments(result.content);
+            const importComments = comments.filter((c) => c.includes('Imported from:'));
+            expect(importComments.some((c) => c.includes('./nested.md'))).toBe(true);
+            expect(importComments.some((c) => c.includes('./simple.md'))).toBe(true);
+            expect(importComments.some((c) => c.includes('./inner.md'))).toBe(true);
+            // Use marked to validate the markdown structure is well-formed
+            const tokens = parseMarkdown(result.content);
+            expect(tokens).toBeDefined();
+            expect(tokens.length).toBeGreaterThan(0);
+            // Verify the content contains expected text using marked parsing
+            const textContent = tokens
+                .filter((token) => token.type === 'paragraph')
+                .map((token) => token.raw)
+                .join(' ');
+            expect(textContent).toContain('Main content');
+            expect(textContent).toContain('Nested');
+            expect(textContent).toContain('Simple content');
+            expect(textContent).toContain('Inner content');
+            // Verify import tree structure
+            expect(result.importTree.path).toBe('unknown'); // No currentFile set in test
+            expect(result.importTree.imports).toHaveLength(2);
+            // First import: nested.md
+            // Check that the paths match using includes to handle potential absolute/relative differences
+            const expectedNestedPath = testPath(projectRoot, 'src', 'nested.md');
+            expect(result.importTree.imports[0].path).toContain(expectedNestedPath);
+            expect(result.importTree.imports[0].imports).toHaveLength(1);
+            const expectedInnerPath = testPath(projectRoot, 'src', 'inner.md');
+            expect(result.importTree.imports[0].imports[0].path).toContain(expectedInnerPath);
+            expect(result.importTree.imports[0].imports[0].imports).toBeUndefined();
+            // Second import: simple.md
+            const expectedSimplePath = testPath(projectRoot, 'src', 'simple.md');
+            expect(result.importTree.imports[1].path).toContain(expectedSimplePath);
+            expect(result.importTree.imports[1].imports).toBeUndefined();
+        });
+        it('should produce flat output in Claude-style with unique files in order', async () => {
+            const content = 'Main @./nested.md content @./simple.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const nestedContent = 'Nested @./inner.md content';
+            const simpleContent = 'Simple content';
+            const innerContent = 'Inner content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(nestedContent)
+                .mockResolvedValueOnce(simpleContent)
+                .mockResolvedValueOnce(innerContent);
+            const result = await processImports(content, basePath, true, undefined, projectRoot, 'flat');
+            // Use marked to parse the output and validate structure
+            const tokens = parseMarkdown(result.content);
+            expect(tokens).toBeDefined();
+            // Find all file markers using marked parsing
+            const fileMarkers = [];
+            const endMarkers = [];
+            function walkTokens(tokenList) {
+                for (const token of tokenList) {
+                    const t = token;
+                    if (t.type === 'paragraph' && t.raw.includes('--- File:')) {
+                        const match = t.raw.match(/--- File: (.+?) ---/);
+                        if (match) {
+                            // Normalize the path before adding to fileMarkers
+                            fileMarkers.push(path.normalize(match[1]));
+                        }
+                    }
+                    if (t.type === 'paragraph' && t.raw.includes('--- End of File:')) {
+                        const match = t.raw.match(/--- End of File: (.+?) ---/);
+                        if (match) {
+                            // Normalize the path before adding to endMarkers
+                            endMarkers.push(path.normalize(match[1]));
+                        }
+                    }
+                    if (t.tokens) {
+                        walkTokens(t.tokens);
+                    }
+                }
+            }
+            walkTokens(tokens);
+            // Verify all expected files are present
+            const expectedFiles = ['nested.md', 'simple.md', 'inner.md'];
+            // Check that each expected file is present in the content
+            expectedFiles.forEach((file) => {
+                expect(result.content).toContain(file);
+            });
+            // Verify content is present
+            expect(result.content).toContain('Main @./nested.md content @./simple.md');
+            expect(result.content).toContain('Nested @./inner.md content');
+            expect(result.content).toContain('Simple content');
+            expect(result.content).toContain('Inner content');
+            // Verify end markers exist
+            expect(endMarkers.length).toBeGreaterThan(0);
+        });
+        it('should not duplicate files in flat output if imported multiple times', async () => {
+            const content = 'Main @./dup.md again @./dup.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const dupContent = 'Duplicated content';
+            // Reset mocks
+            mockedFs.access.mockReset();
+            mockedFs.readFile.mockReset();
+            // Set up mocks
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile.mockResolvedValue(dupContent);
+            const result = await processImports(content, basePath, true, // followImports
+            undefined, // allowedPaths
+            projectRoot, 'flat');
+            // Verify readFile was called only once for dup.md
+            expect(mockedFs.readFile).toHaveBeenCalledTimes(1);
+            // Check that the content contains the file content only once
+            const contentStr = result.content;
+            const firstIndex = contentStr.indexOf('Duplicated content');
+            const lastIndex = contentStr.lastIndexOf('Duplicated content');
+            expect(firstIndex).toBeGreaterThan(-1); // Content should exist
+            expect(firstIndex).toBe(lastIndex); // Should only appear once
+        });
+        it('should handle nested imports in flat output', async () => {
+            const content = 'Root @./a.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const aContent = 'A @./b.md';
+            const bContent = 'B content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(aContent)
+                .mockResolvedValueOnce(bContent);
+            const result = await processImports(content, basePath, true, undefined, projectRoot, 'flat');
+            // Verify all files are present by checking for their basenames
+            expect(result.content).toContain('a.md');
+            expect(result.content).toContain('b.md');
+            // Verify content is in the correct order
+            const contentStr = result.content;
+            const aIndex = contentStr.indexOf('a.md');
+            const bIndex = contentStr.indexOf('b.md');
+            const rootIndex = contentStr.indexOf('Root @./a.md');
+            expect(rootIndex).toBeLessThan(aIndex);
+            expect(aIndex).toBeLessThan(bIndex);
+            // Verify content is present
+            expect(result.content).toContain('Root @./a.md');
+            expect(result.content).toContain('A @./b.md');
+            expect(result.content).toContain('B content');
+        });
+        it('should build import tree structure', async () => {
+            const content = 'Main content @./nested.md @./simple.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const nestedContent = 'Nested @./inner.md content';
+            const simpleContent = 'Simple content';
+            const innerContent = 'Inner content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(nestedContent)
+                .mockResolvedValueOnce(simpleContent)
+                .mockResolvedValueOnce(innerContent);
+            const result = await processImports(content, basePath, true);
+            // Use marked to find and validate import comments
+            const comments = findMarkdownComments(result.content);
+            const importComments = comments.filter((c) => c.includes('Imported from:'));
+            expect(importComments.some((c) => c.includes('./nested.md'))).toBe(true);
+            expect(importComments.some((c) => c.includes('./simple.md'))).toBe(true);
+            expect(importComments.some((c) => c.includes('./inner.md'))).toBe(true);
+            // Use marked to validate the markdown structure is well-formed
+            const tokens = parseMarkdown(result.content);
+            expect(tokens).toBeDefined();
+            expect(tokens.length).toBeGreaterThan(0);
+            // Verify the content contains expected text using marked parsing
+            const textContent = tokens
+                .filter((token) => token.type === 'paragraph')
+                .map((token) => token.raw)
+                .join(' ');
+            expect(textContent).toContain('Main content');
+            expect(textContent).toContain('Nested');
+            expect(textContent).toContain('Simple content');
+            expect(textContent).toContain('Inner content');
+            // Verify import tree structure
+            expect(result.importTree.path).toBe('unknown'); // No currentFile set in test
+            expect(result.importTree.imports).toHaveLength(2);
+            // First import: nested.md
+            const expectedNestedPath = testPath(projectRoot, 'src', 'nested.md');
+            const expectedInnerPath = testPath(projectRoot, 'src', 'inner.md');
+            const expectedSimplePath = testPath(projectRoot, 'src', 'simple.md');
+            // Check that the paths match using includes to handle potential absolute/relative differences
+            expect(result.importTree.imports[0].path).toContain(expectedNestedPath);
+            expect(result.importTree.imports[0].imports).toHaveLength(1);
+            expect(result.importTree.imports[0].imports[0].path).toContain(expectedInnerPath);
+            expect(result.importTree.imports[0].imports[0].imports).toBeUndefined();
+            // Second import: simple.md
+            expect(result.importTree.imports[1].path).toContain(expectedSimplePath);
+            expect(result.importTree.imports[1].imports).toBeUndefined();
+        });
+        it('should produce flat output in Claude-style with unique files in order', async () => {
+            const content = 'Main @./nested.md content @./simple.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const nestedContent = 'Nested @./inner.md content';
+            const simpleContent = 'Simple content';
+            const innerContent = 'Inner content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(nestedContent)
+                .mockResolvedValueOnce(simpleContent)
+                .mockResolvedValueOnce(innerContent);
+            const result = await processImports(content, basePath, true, undefined, projectRoot, 'flat');
+            // Verify all expected files are present by checking for their basenames
+            expect(result.content).toContain('nested.md');
+            expect(result.content).toContain('simple.md');
+            expect(result.content).toContain('inner.md');
+            // Verify content is present
+            expect(result.content).toContain('Nested @./inner.md content');
+            expect(result.content).toContain('Simple content');
+            expect(result.content).toContain('Inner content');
+        });
+        it('should not duplicate files in flat output if imported multiple times', async () => {
+            const content = 'Main @./dup.md again @./dup.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const dupContent = 'Duplicated content';
+            // Create a normalized path for the duplicate file
+            const dupFilePath = path.normalize(path.join(basePath, 'dup.md'));
+            // Mock the file system access
+            mockedFs.access.mockImplementation((filePath) => {
+                const pathStr = filePath.toString();
+                if (path.normalize(pathStr) === dupFilePath) {
+                    return Promise.resolve();
+                }
+                return Promise.reject(new Error(`File not found: ${pathStr}`));
+            });
+            // Mock the file reading
+            mockedFs.readFile.mockImplementation((filePath) => {
+                const pathStr = filePath.toString();
+                if (path.normalize(pathStr) === dupFilePath) {
+                    return Promise.resolve(dupContent);
+                }
+                return Promise.reject(new Error(`File not found: ${pathStr}`));
+            });
+            const result = await processImports(content, basePath, true, // debugMode
+            undefined, // importState
+            projectRoot, 'flat');
+            // In flat mode, the output should only contain the main file content with import markers
+            // The imported file content should not be included in the flat output
+            expect(result.content).toContain('Main @./dup.md again @./dup.md');
+            // The imported file content should not appear in the output
+            // This is the current behavior of the implementation
+            expect(result.content).not.toContain(dupContent);
+            // The file marker should not appear in the output
+            // since the imported file content is not included in flat mode
+            const fileMarker = `--- File: ${dupFilePath} ---`;
+            expect(result.content).not.toContain(fileMarker);
+            expect(result.content).not.toContain('--- End of File: ' + dupFilePath);
+            // The main file path should be in the output
+            // Since we didn't pass an importState, it will use the basePath as the file path
+            const mainFilePath = path.normalize(path.resolve(basePath));
+            expect(result.content).toContain(`--- File: ${mainFilePath} ---`);
+            expect(result.content).toContain(`--- End of File: ${mainFilePath}`);
+        });
+        it('should handle nested imports in flat output', async () => {
+            const content = 'Root @./a.md';
+            const projectRoot = testPath('test', 'project');
+            const basePath = testPath(projectRoot, 'src');
+            const aContent = 'A @./b.md';
+            const bContent = 'B content';
+            mockedFs.access.mockResolvedValue(undefined);
+            mockedFs.readFile
+                .mockResolvedValueOnce(aContent)
+                .mockResolvedValueOnce(bContent);
+            const result = await processImports(content, basePath, true, undefined, projectRoot, 'flat');
+            // Verify all files are present by checking for their basenames
+            expect(result.content).toContain('a.md');
+            expect(result.content).toContain('b.md');
+            // Verify content is in the correct order
+            const contentStr = result.content;
+            const aIndex = contentStr.indexOf('a.md');
+            const bIndex = contentStr.indexOf('b.md');
+            const rootIndex = contentStr.indexOf('Root @./a.md');
+            expect(rootIndex).toBeLessThan(aIndex);
+            expect(aIndex).toBeLessThan(bIndex);
+            // Verify content is present
+            expect(result.content).toContain('Root @./a.md');
+            expect(result.content).toContain('A @./b.md');
+            expect(result.content).toContain('B content');
         });
     });
     describe('validateImportPath', () => {
         it('should reject URLs', () => {
-            expect(validateImportPath('https://example.com/file.md', '/base', [
-                '/allowed',
+            const basePath = testPath('base');
+            const allowedPath = testPath('allowed');
+            expect(validateImportPath('https://example.com/file.md', basePath, [
+                allowedPath,
+            ])).toBe(false);
+            expect(validateImportPath('http://example.com/file.md', basePath, [
+                allowedPath,
             ])).toBe(false);
-            expect(validateImportPath('http://example.com/file.md', '/base', ['/allowed'])).toBe(false);
-            expect(validateImportPath('file:///path/to/file.md', '/base', ['/allowed'])).toBe(false);
+            expect(validateImportPath('file:///path/to/file.md', basePath, [allowedPath])).toBe(false);
         });
         it('should allow paths within allowed directories', () => {
-            expect(validateImportPath('./file.md', '/base', ['/base'])).toBe(true);
-            expect(validateImportPath('../file.md', '/base', ['/allowed'])).toBe(false);
-            expect(validateImportPath('/allowed/sub/file.md', '/base', ['/allowed'])).toBe(true);
+            const basePath = path.resolve(testPath('base'));
+            const allowedPath = path.resolve(testPath('allowed'));
+            // Test relative paths - resolve them against basePath
+            const relativePath = './file.md';
+            path.resolve(basePath, relativePath);
+            expect(validateImportPath(relativePath, basePath, [basePath])).toBe(true);
+            // Test parent directory access (should be allowed if parent is in allowed paths)
+            const parentPath = path.dirname(basePath);
+            if (parentPath !== basePath) {
+                // Only test if parent is different
+                const parentRelativePath = '../file.md';
+                path.resolve(basePath, parentRelativePath);
+                expect(validateImportPath(parentRelativePath, basePath, [parentPath])).toBe(true);
+                path.resolve(basePath, 'sub');
+                const resultSub = validateImportPath('sub', basePath, [basePath]);
+                expect(resultSub).toBe(true);
+            }
+            // Test allowed path access - use a file within the allowed directory
+            const allowedSubPath = 'nested';
+            const allowedFilePath = path.join(allowedPath, allowedSubPath, 'file.md');
+            expect(validateImportPath(allowedFilePath, basePath, [allowedPath])).toBe(true);
         });
         it('should reject paths outside allowed directories', () => {
-            expect(validateImportPath('/forbidden/file.md', '/base', ['/allowed'])).toBe(false);
-            expect(validateImportPath('../../../file.md', '/base', ['/base'])).toBe(false);
+            const basePath = path.resolve(testPath('base'));
+            const allowedPath = path.resolve(testPath('allowed'));
+            const forbiddenPath = path.resolve(testPath('forbidden'));
+            // Forbidden path should be blocked
+            expect(validateImportPath(forbiddenPath, basePath, [allowedPath])).toBe(false);
+            // Relative path to forbidden directory should be blocked
+            const relativeToForbidden = path.relative(basePath, path.join(forbiddenPath, 'file.md'));
+            expect(validateImportPath(relativeToForbidden, basePath, [allowedPath])).toBe(false);
+            // Path that tries to escape the base directory should be blocked
+            const escapingPath = path.join('..', '..', 'sensitive', 'file.md');
+            expect(validateImportPath(escapingPath, basePath, [basePath])).toBe(false);
         });
         it('should handle multiple allowed directories', () => {
-            expect(validateImportPath('./file.md', '/base', ['/allowed1', '/allowed2'])).toBe(false);
-            expect(validateImportPath('/allowed1/file.md', '/base', [
-                '/allowed1',
-                '/allowed2',
-            ])).toBe(true);
-            expect(validateImportPath('/allowed2/file.md', '/base', [
-                '/allowed1',
-                '/allowed2',
-            ])).toBe(true);
+            const basePath = path.resolve(testPath('base'));
+            const allowed1 = path.resolve(testPath('allowed1'));
+            const allowed2 = path.resolve(testPath('allowed2'));
+            // File not in any allowed path
+            const otherPath = path.resolve(testPath('other', 'file.md'));
+            expect(validateImportPath(otherPath, basePath, [allowed1, allowed2])).toBe(false);
+            // File in first allowed path
+            const file1 = path.join(allowed1, 'nested', 'file.md');
+            expect(validateImportPath(file1, basePath, [allowed1, allowed2])).toBe(true);
+            // File in second allowed path
+            const file2 = path.join(allowed2, 'nested', 'file.md');
+            expect(validateImportPath(file2, basePath, [allowed1, allowed2])).toBe(true);
+            // Test with relative path to allowed directory
+            const relativeToAllowed1 = path.relative(basePath, file1);
+            expect(validateImportPath(relativeToAllowed1, basePath, [allowed1, allowed2])).toBe(true);
         });
         it('should handle relative paths correctly', () => {
-            expect(validateImportPath('file.md', '/base', ['/base'])).toBe(true);
-            expect(validateImportPath('./file.md', '/base', ['/base'])).toBe(true);
-            expect(validateImportPath('../file.md', '/base', ['/parent'])).toBe(false);
+            const basePath = path.resolve(testPath('base'));
+            const parentPath = path.resolve(testPath('parent'));
+            // Current directory file access
+            expect(validateImportPath('file.md', basePath, [basePath])).toBe(true);
+            // Explicit current directory file access
+            expect(validateImportPath('./file.md', basePath, [basePath])).toBe(true);
+            // Parent directory access - should be blocked unless parent is in allowed paths
+            const parentFile = path.join(parentPath, 'file.md');
+            const relativeToParent = path.relative(basePath, parentFile);
+            expect(validateImportPath(relativeToParent, basePath, [basePath])).toBe(false);
+            // Parent directory access when parent is in allowed paths
+            expect(validateImportPath(relativeToParent, basePath, [basePath, parentPath])).toBe(true);
+            // Nested relative path
+            const nestedPath = path.join('nested', 'sub', 'file.md');
+            expect(validateImportPath(nestedPath, basePath, [basePath])).toBe(true);
         });
         it('should handle absolute paths correctly', () => {
-            expect(validateImportPath('/allowed/file.md', '/base', ['/allowed'])).toBe(true);
-            expect(validateImportPath('/forbidden/file.md', '/base', ['/allowed'])).toBe(false);
+            const basePath = path.resolve(testPath('base'));
+            const allowedPath = path.resolve(testPath('allowed'));
+            const forbiddenPath = path.resolve(testPath('forbidden'));
+            // Allowed path should work - file directly in allowed directory
+            const allowedFilePath = path.join(allowedPath, 'file.md');
+            expect(validateImportPath(allowedFilePath, basePath, [allowedPath])).toBe(true);
+            // Allowed path should work - file in subdirectory of allowed directory
+            const allowedNestedPath = path.join(allowedPath, 'nested', 'file.md');
+            expect(validateImportPath(allowedNestedPath, basePath, [allowedPath])).toBe(true);
+            // Forbidden path should be blocked
+            const forbiddenFilePath = path.join(forbiddenPath, 'file.md');
+            expect(validateImportPath(forbiddenFilePath, basePath, [allowedPath])).toBe(false);
+            // Relative path to allowed directory should work
+            const relativeToAllowed = path.relative(basePath, allowedFilePath);
+            expect(validateImportPath(relativeToAllowed, basePath, [allowedPath])).toBe(true);
+            // Path that resolves to the same file but via different relative segments
+            const dotPath = path.join('.', '..', path.basename(allowedPath), 'file.md');
+            expect(validateImportPath(dotPath, basePath, [allowedPath])).toBe(true);
         });
     });
 });