feat: implement Phase 1 — linear resource analysis, violation detection, and wrapper generation

Rewrites the generic iseriser scaffold into a working ephapaxiser tool that:
- Parses source files to find resource allocation/deallocation call sites (parser.rs)
- Tracks ownership state and detects leaks, double-frees, use-after-free (analyzer.rs)
- Generates Ephapax linear type wrapper structs enforcing exactly-once usage (wrapper_gen.rs)
- Provides a domain-specific manifest format (ephapaxiser.toml) with resource definitions
- Defines core ABI types: ResourceKind, LinearResource, OwnershipState, Violation, AnalysisResult

All 45 tests pass (17 lib unit + 17 bin unit + 11 integration).
Includes examples/safe-files/ with intentional bugs for demonstration.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: hyperpolymath

Cargo.lock

@@ -7,7 +7,7 @@ authors = ["Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>"]
 description = "Enforce single-use linear type semantics on resources in existing code via Ephapax"
 license = "PMPL-1.0-or-later"
 repository = "https://github.com/hyperpolymath/ephapaxiser"
-keywords = ["ephapax", "acceleration", "code-generation"]
+keywords = ["ephapax", "linear-types", "resource-safety", "code-generation"]
 categories = ["command-line-utilities", "development-tools"]
 
 [dependencies]
@@ -16,7 +16,7 @@ serde = { version = "1", features = ["derive"] }
 toml = "0.8"
 anyhow = "1"
 thiserror = "2"
-handlebars = "6"
+serde_json = "1"
 walkdir = "2"
 
 [dev-dependencies]

Cargo.toml

@@ -0,0 +1,35 @@
+# SPDX-License-Identifier: PMPL-1.0-or-later
+# Example ephapaxiser manifest — demonstrates resource tracking for file operations.
+#
+# This manifest configures ephapaxiser to analyse file_ops.rs for proper
+# file descriptor handling (open/close pairs).
+
+[project]
+name = "safe-files-example"
+
+# Source files to analyse.
+[[sources]]
+name = "file-handler"
+path = "src/file_ops.rs"
+language = "rust"
+
+# Resource definitions — file descriptors with open/close pair.
+[[resources]]
+name = "FileHandle"
+allocator = "open"
+deallocator = "close"
+kind = "file-descriptor"
+
+# Also track database connections in this example.
+[[resources]]
+name = "DbConnection"
+allocator = "connect"
+deallocator = "disconnect"
+kind = "db-connection"
+
+# Analysis configuration.
+[analysis]
+detect-leaks = true
+detect-double-free = true
+detect-use-after-free = true
+report-format = "text"

examples/safe-files/ephapaxiser.toml

@@ -0,0 +1,40 @@
+// SPDX-License-Identifier: PMPL-1.0-or-later
+// Copyright (c) 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+//
+// Example source file for ephapaxiser analysis.
+//
+// This file demonstrates various resource usage patterns — some correct, some
+// intentionally buggy — so that ephapaxiser can detect violations.
+
+/// Correct usage: file is opened and properly closed.
+fn correct_file_usage() {
+    let fd = open("data.txt");
+    // ... use the file ...
+    close(fd);
+}
+
+/// BUG: Resource leak — file is opened but never closed.
+fn leaky_file_usage() {
+    let fd = open("leaked.txt");
+    // ... forgot to close ...
+}
+
+/// BUG: Double-free — file is closed twice.
+fn double_close() {
+    let fd = open("double.txt");
+    close(fd);
+    close(fd);
+}
+
+/// Correct database usage: connection is opened and properly disconnected.
+fn correct_db_usage() {
+    let conn = connect("postgres://localhost/mydb");
+    // ... query the database ...
+    disconnect(conn);
+}
+
+/// BUG: Database connection leak.
+fn leaky_db_usage() {
+    let conn = connect("postgres://localhost/mydb");
+    // ... forgot to disconnect ...
+}