Enhance CLI functionality and improve common utilities

- Added new commands to the CLI for dumping regions, renaming functions by address, and setting various types of comments.
- Implemented JSON output formatting for CLI commands.
- Introduced functions for decompiling and disassembling functions, as well as retrieving cross-references.
- Enhanced common utilities with functions for reading memory regions, iterating Java items, and managing function metadata.
- Added suppress_output context manager to hide process output during Ghidra startup.
- Updated existing functions to improve error handling and output formatting.

.github/skills/pyghidra-ghidra-ops/SKILL.md

@@ -1,12 +1,14 @@
 # PyGhidra Ghidra Ops
 
-Use this skill when Ghidra MCP is missing a needed write operation and you need native CPython access to the Ghidra API for the local Crusader project.
+Use this skill when Ghidra MCP is missing a needed operation and you need native CPython access to the Ghidra API for the local Crusader project.
 
 ## Use Cases
 
 - Create or delete functions in `CRUSADER-RAW.EXE`.
 - Apply small batched repairs driven by verified addresses.
 - Add comments or rename functions by address from a repeatable JSON plan.
+- Decompile or disassemble functions without switching back to the MCP server.
+- Query function metadata, search by name, and inspect xrefs from the same local CLI.
 - Inspect project root files to confirm the program name/path before running edits.
 
 ## Workspace Defaults
@@ -56,6 +58,63 @@ Rename a function by entry address:
 .\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader rename-function --entry 0006:02cc --name entity_class_get_flag20
 ```
 
+MCP-style read/query commands are also available from the same CLI:
+
+```powershell
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader get-function-by-address --address 000a:48ff
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader get-function-containing --address 000a:4901
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader decompile-function-by-address --address 000a:48ff
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader disassemble-function --address 000a:48ff
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader read-region --start 000a:48ff --end 000a:4912
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader search-functions-by-name --query rng_
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-strings --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-imports --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-exports --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-namespaces --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-segments --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-data-items --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader list-classes --limit 20
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader get-xrefs-to --address 000a:48ff
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader get-function-xrefs --name rng_next_modulo
+```
+
+All commands also support structured output for scripting:
+
+```powershell
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader --format json get-function-by-address --address 000a:48ff
+```
+
+For ad hoc investigation, prefer `run-script` over multiline `python -c` or pasted PowerShell here-strings. It avoids leaving the shared shell stuck in an unfinished string/block state:
+
+```powershell
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader run-script --script .\pyghidra_plans\inspect_rng.py --read-only
+```
+
+Script globals available inside `run-script`:
+
+```python
+config
+project
+program
+helpers["get_function"]
+helpers["get_function_containing"]
+helpers["decompile_function"]
+helpers["disassemble_function"]
+helpers["get_xrefs_to"]
+helpers["get_xrefs_from"]
+helpers["read_region_bytes"]
+helpers["rename_function"]
+helpers["set_comment"]
+```
+
+Write-side MCP-style aliases are available too:
+
+```powershell
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader rename-function-by-address --entry 000a:48ff --name rng_next_modulo
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader set-decompiler-comment --address 000a:48ff --text "Returns RNG output modulo the requested bound."
+.\.venv-pyghidra311\Scripts\python.exe -m tools.pyghidra_crusader set-disassembly-comment --address 000a:48ff --text "Modulo wrapper around rng_advance_state"
+```
+
 Apply a small JSON plan:
 
 ```json
@@ -109,4 +168,9 @@ Dry-run a plan before touching the project:
 
 - Address strings accept raw `SSSS:OOOO` form or plain integers such as `0x75a90`.
 - The CLI tries a few root folder path variants when opening the program so it can tolerate minor project path differences.
-- Plan files support `remove_functions`, `rename_functions`, `create_functions`, `comments`, and `assert_functions`.
+- Plan files support `remove_functions`, `rename_functions`, `create_functions`, `comments`, and `assert_functions`.
+- `set-decompiler-comment` maps to a pre-comment and `set-disassembly-comment` maps to an EOL comment.
+- Read/query commands open the program read-only; create/rename/comment/plan commands still require the project to be writable.
+- `run-script --read-only` is the safest way to do one-off inspection without getting the shared PowerShell session stuck in a multiline Python string.
+- `read-region` now reads bytes one address at a time instead of relying on a bulk `getBytes` path that produced misleading all-zero results in this project under PyGhidra.
+- PyGhidra startup now suppresses the noisy local GhidraMCP `Module.manifest` warnings during normal CLI operation.