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[fix] I/P: Fix connection failure during some remote builds#201

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hanno-becker wants to merge 9 commits intomainfrom
ip_build_fix
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[fix] I/P: Fix connection failure during some remote builds#201
hanno-becker wants to merge 9 commits intomainfrom
ip_build_fix

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@hanno-becker hanno-becker commented Mar 29, 2026

Symptom: Sessions with multiple theories blocks in ROOT failed when built remotely via I/P, with repeated "Connection refused: failed to open socket 127.0.0.1:" errors. The build completed all theory loading but exited with rc=1.

Issue: When proxying a build to a remote machine, the proxy rewrites bash_process_address in PIDE messages so that the remote ML process connects to a remote Bash.Server instead of the local one. The build_session message carries a separate Options object per theory group, each containing bash_process_address. The rewrite only replaced the first occurrence (count=1), leaving subsequent groups with the unrewritten local address.

Fix: Remove the count limit from replace() for both bash_process_address and bash_process_password, so all theory groups are rewritten.

Issue #, if available:

Description of changes:

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Symptom: Sessions with multiple `theories` blocks in ROOT failed when
built remotely via I/P, with repeated "Connection refused: failed to
open socket 127.0.0.1:<port>" errors. The build completed all theory
loading but exited with rc=1.

Issue: When proxying a build to a remote machine, the proxy rewrites
bash_process_address in PIDE messages so that the remote ML process
connects to a remote Bash.Server instead of the local one. The
build_session message carries a separate Options object per theory
group, each containing bash_process_address. The rewrite only replaced
the first occurrence (count=1), leaving subsequent groups with the
unrewritten local address.

Fix: Remove the count limit from replace() for both bash_process_address
and bash_process_password, so all theory groups are rewritten.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
Source file verification was skipped entirely when the variable was
missing. Now defaults to the resolved --dir (or pwd), shows a warning,
and proceeds with source status reporting.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
This allows an agent with I/R MCP connection to spawn
multiple subagents working concurrently in separate REPLs.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
MCP clients can now use \<Rightarrow> and ⇒ interchangeably in
pattern, old_str, new_str, and content parameters. Whitespace
differences (extra spaces, tabs) are also tolerated during matching.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
Without timing data from REPL steps, agents have a hard time optimizing
proofs for performance.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
LLM-based MCP clients to I/R are sensitive to the amount of information
the receive, but the I/R output contains a lot of noise, including:

- Every evaluation is suffixed with `val it = (): unit`
- 'Duplicate simpset' warnings

This commit adds an extensible noise filter to I/R to increase the
information density of the response to the LLM.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
Timeout was a single global Synchronized.var shared across all REPLs,
so one MCP client changing it affected every other concurrent session.
Move it to a per-REPL field: init/init_from_document default to 10s,
fork inherits from parent, and Ir.timeout now takes a REPL ID.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
Symptom: when multiple MCP clients maintain persistent TCP connections to
I/R (e.g. repl.py's default pool of 5 + 1 console = 6 connections),
Isabelle/jEdit becomes sluggish or unresponsive — PIDE proof checking
and interactive editing stall even though the REPL connections are idle.

Analysis: I/R's TCP server used Future.fork (tcp_handler.ML) and
Future.forks (ml_repl.ML) to spawn connection handler and accept loop
threads.  Isabelle's Future system is a fixed-size worker thread pool
(typically max_threads = 8), not raw OS threads.  Each Future.fork body
that blocks on socket I/O permanently occupies a worker slot — the
worker cannot return to the pool to pick up other tasks.  With 6
persistent connections + 1 accept loop, 7 of 8 worker threads are
parked on blocking reads or Synchronized.guarded_access, leaving a
single worker for all PIDE tasks and I/R eval futures combined.

The eval futures themselves were already correctly prioritized at
ir_pri = ~1 (below PIDE's >= 0), but this was moot when no workers
were available to execute them.

Fix: replace Future.fork/Future.forks with Isabelle_Thread.fork for all
I/O-bound threads (TCP connection handlers and accept loop).
Isabelle_Thread creates standalone OS threads outside the Future worker
pool — the standard Isabelle idiom for I/O threads (cf.
Message_Channel.make in message_channel.ML).  Connection threads can
block on socket I/O indefinitely without reducing the pool's capacity.
The full worker pool remains available for PIDE and I/R eval futures.

Output routing is unaffected: connection handlers use direct
Message_Channel.message calls (not Private_Output), while eval futures
still run in the worker pool with correct Future group ancestry
(ir_group → conn_group → cmd_group) for find_connection_message().

Added prominent warnings at is_server_context(), connection_serve(), and
eval_in_group() documenting that Private_Output wrappers (writeln,
warning, etc.) only route correctly on Future worker threads — code on
connection Isabelle_Threads must use the direct `message` function.

Signed-off-by: Hanno Becker <beckphan@amazon.co.uk>
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